Closed mavino closed 5 years ago
PolinaBevad
commented
5 years ago Mariano, hello!
I assume that this can happen because there is no region or BED file on the command line. It should be set at the end of the main command (before R script) as described here: https://github.com/AstraZeneca-NGS/VarDict/blob/master/README.rst#quick-start Could you please try running it with BED?
mavino
commented
5 years ago Dear @PolinaBevad, I have included the bed file of my tumoral sample and I get still the same error:
dekoterlab@Fred:~/Downloads/VarDict-master$ perl vardict -G /home/dekoterlab/mm10/UCSC_mm10.fa -f 0.01 -N tumor_sample_name -b "/media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/HI.4777.004.SSXTLI_46.932_Thy.bam|/media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/HI.4777.004.SSXTLI_45.932_Tail.bam" -c 1 -S 2 -E 3 -g 4 /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/Galaxy86-[SAM-to-BAM_932_Thy_\(as_BED\)].bed | R testsomatic.R | perl var2vcf_paired.pl -N "932_Thy|932_Tail" -f 0.01
Fatal error: you must specify '--save', '--no-save' or '--vanilla'
Use of uninitialized value $chr in hash element at var2vcf_paired.pl line 33, <> line 1.
Use of uninitialized value $a[3] in hash element at var2vcf_paired.pl line 33, <> line 1.
Use of uninitialized value $chr in hash element at var2vcf_paired.pl line 33, <> line 2.
Use of uninitialized value $a[3] in hash element at var2vcf_paired.pl line 33, <> line 2.
Use of uninitialized value $sample in concatenation (.) or string at var2vcf_paired.pl line 35, <> line 2.
##fileformat=VCFv4.1
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">
##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">
##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
##FILTER=<ID=Bias,Description="Strand Bias">
##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">
##FILTER=<ID=d5,Description="Total Depth < 5">
##FILTER=<ID=v3,Description="Var Depth < 3">
##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">
##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">
##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">
##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">
##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 932_Thy 932_Tail
Argument "" isn't numeric in sort at var2vcf_paired.pl line 107, <> line 2.
Use of uninitialized value in numeric comparison (<=>) at var2vcf_paired.pl line 113, <> line 2.
Use of uninitialized value in numeric comparison (<=>) at var2vcf_paired.pl line 113, <> line 2.
Use of uninitialized value $rrev1 in addition (+) at var2vcf_paired.pl line 119, <> line 2.
Use of uninitialized value $rfwd1 in addition (+) at var2vcf_paired.pl line 119, <> line 2.
Use of uninitialized value $rrev2 in addition (+) at var2vcf_paired.pl line 120, <> line 2.
Use of uninitialized value $rfwd2 in addition (+) at var2vcf_paired.pl line 120, <> line 2.
Use of uninitialized value $chrt in concatenation (.) or string at var2vcf_paired.pl line 121, <> line 2.
Use of uninitialized value $start in concatenation (.) or string at var2vcf_paired.pl line 121, <> line 2.
Use of uninitialized value $end in concatenation (.) or string at var2vcf_paired.pl line 121, <> line 2.
Use of uninitialized value $ref in concatenation (.) or string at var2vcf_paired.pl line 121, <> line 2.
Use of uninitialized value $alt in concatenation (.) or string at var2vcf_paired.pl line 121, <> line 2.
Use of uninitialized value $chrt in concatenation (.) or string at var2vcf_paired.pl line 122, <> line 2.
Use of uninitialized value $start in concatenation (.) or string at var2vcf_paired.pl line 122, <> line 2.
Use of uninitialized value $end in concatenation (.) or string at var2vcf_paired.pl line 122, <> line 2.
Use of uninitialized value $ref in concatenation (.) or string at var2vcf_paired.pl line 122, <> line 2.
Use of uninitialized value $alt in concatenation (.) or string at var2vcf_paired.pl line 122, <> line 2.
Use of uninitialized value $oddratio1 in string eq at var2vcf_paired.pl line 127, <> line 2.
Use of uninitialized value $oddratio1 in numeric lt (<) at var2vcf_paired.pl line 129, <> line 2.
Use of uninitialized value $oddratio1 in numeric gt (>) at var2vcf_paired.pl line 129, <> line 2.
Use of uninitialized value $oddratio2 in string eq at var2vcf_paired.pl line 132, <> line 2.
Use of uninitialized value $oddratio2 in numeric lt (<) at var2vcf_paired.pl line 134, <> line 2.
Use of uninitialized value $oddratio2 in numeric gt (>) at var2vcf_paired.pl line 134, <> line 2.
Use of uninitialized value $dp1 in numeric lt (<) at var2vcf_paired.pl line 137, <> line 2.
Use of uninitialized value $status in string eq at var2vcf_paired.pl line 138, <> line 2.
Use of uninitialized value $vd1 in numeric lt (<) at var2vcf_paired.pl line 140, <> line 2.
Use of uninitialized value $status in string eq at var2vcf_paired.pl line 141, <> line 2.
Use of uninitialized value $dp2 in numeric lt (<) at var2vcf_paired.pl line 143, <> line 2.
Use of uninitialized value $vd2 in numeric lt (<) at var2vcf_paired.pl line 144, <> line 2.
Use of uninitialized value $af1 in numeric lt (<) at var2vcf_paired.pl line 146, <> line 2.
Use of uninitialized value $pmean1 in numeric lt (<) at var2vcf_paired.pl line 148, <> line 2.
Use of uninitialized value $pstd1 in numeric eq (==) at var2vcf_paired.pl line 149, <> line 2.
Use of uninitialized value $vd1 in numeric lt (<) at var2vcf_paired.pl line 149, <> line 2.
Use of uninitialized value $qual1 in numeric lt (<) at var2vcf_paired.pl line 150, <> line 2.
Use of uninitialized value $mapq1 in numeric lt (<) at var2vcf_paired.pl line 151, <> line 2.
Use of uninitialized value $mapq1 in numeric lt (<) at var2vcf_paired.pl line 152, <> line 2.
Use of uninitialized value $sn1 in numeric lt (<) at var2vcf_paired.pl line 153, <> line 2.
Use of uninitialized value $nm1 in numeric ge (>=) at var2vcf_paired.pl line 154, <> line 2.
Use of uninitialized value $bias1 in string eq at var2vcf_paired.pl line 156, <> line 2.
Use of uninitialized value $af2 in numeric lt (<) at var2vcf_paired.pl line 158, <> line 2.
Use of uninitialized value $pmean2 in numeric lt (<) at var2vcf_paired.pl line 159, <> line 2.
Use of uninitialized value $pstd2 in numeric eq (==) at var2vcf_paired.pl line 160, <> line 2.
Use of uninitialized value $vd2 in numeric lt (<) at var2vcf_paired.pl line 160, <> line 2.
Use of uninitialized value $qual2 in numeric lt (<) at var2vcf_paired.pl line 161, <> line 2.
Use of uninitialized value $mapq2 in numeric lt (<) at var2vcf_paired.pl line 162, <> line 2.
Use of uninitialized value $sn2 in numeric lt (<) at var2vcf_paired.pl line 163, <> line 2.
Use of uninitialized value $nm2 in numeric ge (>=) at var2vcf_paired.pl line 164, <> line 2.
Use of uninitialized value $bias2 in string eq at var2vcf_paired.pl line 166, <> line 2.
Use of uninitialized value $msi in numeric gt (>) at var2vcf_paired.pl line 169, <> line 2.
Use of uninitialized value $msi in numeric gt (>) at var2vcf_paired.pl line 169, <> line 2.
Use of uninitialized value in subtraction (-) at var2vcf_paired.pl line 172, <> line 2.
Use of uninitialized value in subtraction (-) at var2vcf_paired.pl line 172, <> line 2.
Use of uninitialized value $msilen in numeric eq (==) at var2vcf_paired.pl line 172, <> line 2.
Use of uninitialized value $msi in numeric gt (>) at var2vcf_paired.pl line 173, <> line 2.
Use of uninitialized value $msi in numeric gt (>) at var2vcf_paired.pl line 173, <> line 2.
Use of uninitialized value $af1 in subtraction (-) at var2vcf_paired.pl line 198, <> line 2.
Use of uninitialized value $af1 in numeric ge (>=) at var2vcf_paired.pl line 198, <> line 2.
Use of uninitialized value $af1 in numeric ge (>=) at var2vcf_paired.pl line 198, <> line 2.
Use of uninitialized value $af2 in subtraction (-) at var2vcf_paired.pl line 199, <> line 2.
Use of uninitialized value $af2 in numeric ge (>=) at var2vcf_paired.pl line 199, <> line 2.
Use of uninitialized value $af2 in numeric ge (>=) at var2vcf_paired.pl line 199, <> line 2.
Use of uninitialized value $bias1 in substitution (s///) at var2vcf_paired.pl line 200, <> line 2.
Use of uninitialized value $bias2 in substitution (s///) at var2vcf_paired.pl line 201, <> line 2.
Use of uninitialized value $vd2 in numeric gt (>) at var2vcf_paired.pl line 202, <> line 2.
Use of uninitialized value $vd1 in numeric gt (>) at var2vcf_paired.pl line 202, <> line 2.
Use of uninitialized value $vd2 in log at var2vcf_paired.pl line 202, <> line 2.
Can't take log of 0 at var2vcf_paired.pl line 202, <> line 2.@mavino, hello, Did you install R with Rserve? I guess it can be a problem of R environment, not the VarDict issue. Could you try to run Rserve with option --no-save, as described here: https://stackoverflow.com/questions/28792399/rserve-error-in-rstudio
mavino
commented
5 years ago R was already installed and I ran vardict with command '--no-save'...however still having problems:
perl vardict -G /home/dekoterlab/mm10/UCSC_mm10.fa -f 0.01 -N tumor_sample_name -b "/media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/HI.4777.004.SSXTLI_46.932_Thy.bam|/media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/HI.4777.004.SSXTLI_45.932_Tail.bam" -c 1 -S 2 -E 3 -g 4 /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/Galaxy86-[SAM-to-BAM_932_Thy].bed | R testsomatic.R --no-save| perl /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl -N "932_Thy|932_Tail" -f 0.01
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 1.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 1.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 2.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 2.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 3.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 3.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 4.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 4.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 5.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 5.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 6.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 6.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 7.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 7.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 8.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 8.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 9.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 9.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 10.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 10.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 11.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 11.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 12.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 12.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 13.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 13.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 14.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 14.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 15.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 15.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 16.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 16.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 17.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 17.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 18.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 18.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 19.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 19.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 20.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 20.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 21.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 21.
Use of uninitialized value $chr in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 22.
Use of uninitialized value $a[3] in hash element at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 33, <> line 22.
##fileformat=VCFv4.1
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">
##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">
##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
##FILTER=<ID=Bias,Description="Strand Bias">
##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">
##FILTER=<ID=d5,Description="Total Depth < 5">
##FILTER=<ID=v3,Description="Var Depth < 3">
##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">
##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">
##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">
##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">
##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 932_Thy 932_Tail
Argument "" isn't numeric in sort at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 107, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value in numeric comparison (<=>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 113, <> line 22.
Use of uninitialized value $rrev1 in addition (+) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 119, <> line 22.
Use of uninitialized value $rfwd1 in addition (+) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 119, <> line 22.
Use of uninitialized value $rrev2 in addition (+) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 120, <> line 22.
Use of uninitialized value $rfwd2 in addition (+) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 120, <> line 22.
Use of uninitialized value $chrt in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 121, <> line 22.
Use of uninitialized value $start in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 121, <> line 22.
Use of uninitialized value $end in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 121, <> line 22.
Use of uninitialized value $ref in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 121, <> line 22.
Use of uninitialized value $alt in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 121, <> line 22.
Use of uninitialized value $chrt in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 122, <> line 22.
Use of uninitialized value $start in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 122, <> line 22.
Use of uninitialized value $end in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 122, <> line 22.
Use of uninitialized value $ref in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 122, <> line 22.
Use of uninitialized value $alt in concatenation (.) or string at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 122, <> line 22.
Use of uninitialized value $oddratio1 in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 127, <> line 22.
Use of uninitialized value $oddratio1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 129, <> line 22.
Use of uninitialized value $oddratio1 in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 129, <> line 22.
Use of uninitialized value $oddratio2 in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 132, <> line 22.
Use of uninitialized value $oddratio2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 134, <> line 22.
Use of uninitialized value $oddratio2 in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 134, <> line 22.
Use of uninitialized value $dp1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 137, <> line 22.
Use of uninitialized value $status in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 138, <> line 22.
Use of uninitialized value $vd1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 140, <> line 22.
Use of uninitialized value $status in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 141, <> line 22.
Use of uninitialized value $dp2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 143, <> line 22.
Use of uninitialized value $vd2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 144, <> line 22.
Use of uninitialized value $af1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 146, <> line 22.
Use of uninitialized value $pmean1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 148, <> line 22.
Use of uninitialized value $pstd1 in numeric eq (==) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 149, <> line 22.
Use of uninitialized value $vd1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 149, <> line 22.
Use of uninitialized value $qual1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 150, <> line 22.
Use of uninitialized value $mapq1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 151, <> line 22.
Use of uninitialized value $mapq1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 152, <> line 22.
Use of uninitialized value $sn1 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 153, <> line 22.
Use of uninitialized value $nm1 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 154, <> line 22.
Use of uninitialized value $bias1 in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 156, <> line 22.
Use of uninitialized value $af2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 158, <> line 22.
Use of uninitialized value $pmean2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 159, <> line 22.
Use of uninitialized value $pstd2 in numeric eq (==) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 160, <> line 22.
Use of uninitialized value $vd2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 160, <> line 22.
Use of uninitialized value $qual2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 161, <> line 22.
Use of uninitialized value $mapq2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 162, <> line 22.
Use of uninitialized value $sn2 in numeric lt (<) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 163, <> line 22.
Use of uninitialized value $nm2 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 164, <> line 22.
Use of uninitialized value $bias2 in string eq at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 166, <> line 22.
Use of uninitialized value $msi in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 169, <> line 22.
Use of uninitialized value $msi in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 169, <> line 22.
Use of uninitialized value in subtraction (-) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 172, <> line 22.
Use of uninitialized value in subtraction (-) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 172, <> line 22.
Use of uninitialized value $msilen in numeric eq (==) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 172, <> line 22.
Use of uninitialized value $msi in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 173, <> line 22.
Use of uninitialized value $msi in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 173, <> line 22.
Use of uninitialized value $af1 in subtraction (-) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 198, <> line 22.
Use of uninitialized value $af1 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 198, <> line 22.
Use of uninitialized value $af1 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 198, <> line 22.
Use of uninitialized value $af2 in subtraction (-) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 199, <> line 22.
Use of uninitialized value $af2 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 199, <> line 22.
Use of uninitialized value $af2 in numeric ge (>=) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 199, <> line 22.
Use of uninitialized value $bias1 in substitution (s///) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 200, <> line 22.
Use of uninitialized value $bias2 in substitution (s///) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 201, <> line 22.
Use of uninitialized value $vd2 in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 202, <> line 22.
Use of uninitialized value $vd1 in numeric gt (>) at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 202, <> line 22.
Use of uninitialized value $vd2 in log at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 202, <> line 22.
Can't take log of 0 at /media/dekoterlab/SAMSUNG/MichelleLim/MichelleLim/BAMBowTie/BAMwithBAI/var2vcf_paired.pl line 202, <> line 22.@mavino, I think it is problem of R installation, and I guess --no-save must be set in Rserve or Rstudio before running R scripts.
I can check your samples in my environment to be sure if it is R problem and not VarDict. If it is possible, you can send parts of BAM files to reproduce the problem to polina_bevad@epam.com
mavino
commented
5 years ago @PolinaBevad I don't understand what you mean by that.
I mean, I ran the 'vardict' script by calling it through perl in command line, and in my command the R script is called right after (part of the command). Thus, how do I set no-save in Rserve or Rstudio?
Anyways I will try to arrange in sending you the files.
Thank you very much.
PolinaBevad
commented
5 years ago Mariano, hello! Is everything good with your runs? Have you got any VCF files after replacing the fasta (the BAM file you provided was aligned on Mus_musculus.GRCm38.fa)? Please let me know if you have problems with it.
mavino
commented
5 years ago OK the problem was on our side. There were inconsistencies between the reference genome used to map (bult-in ones provided by Galaxy) and the one used to make the bed file after bam (our own genome reference). The two of them were the same version but strangely the order of the chromosomes were not the same. We used ReorderSam from picard to match the bam file with our version of reference genome and that solved the problem. Thank you very much for all the help.
this is my command line:
and I get this error: