jammywwh
commented
1 year ago chr17 39724742 is right, but here is another problem, why "chr17 39724728 . A AGCATACGTGATG" and "chr17 39724742 . A AGCATACGTGATG" have same ref and alt? In my opinion, vardict-java with -3 parameter, it should be "chr17 39724742 . C CATACGTGATGGC", because chr17:39724742 ref is C. anyone else can help me?
hi, when using -3 parameter, i got some confused variants.
reference genome: hg38 vardict-java with -3 parameter , i got this mutation : chr17 39724742 . A AGCATACGTGATG 188 PASS SAMPLE=028032_gDNA;TYPE=Insertion;DP=2012;VD=32;AF=0.0159;BIAS=2:2;REFBIAS=1015:960;VARBIAS=18:14;PMEAN=37.2;PSTD=1;QUAL=37.7;QSTD=1;SBF=0.59883;ODDRATIO=1.2159237372632;MQ=60;SN=64;HIAF=0.0164;ADJAF=0;SHIFT3=14;MSI=2;MSILEN=1;NM=0.1;HICNT=32;HICOV=1946;LSEQ=CCAGGAAGCATACGTGATGG;RSEQ=TGGTGTGGGCTCCCCATATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:2012:32:1975,32:0.0159:1015,960:18,14
without -3 parameter: chr17 39724728 . A AGCATACGTGATG 188 PASS SAMPLE=028032_gDNA;TYPE=Insertion;DP=2012;VD=32;AF=0.0159;BIAS=2:2;REFBIAS=1015:960;VARBIAS=18:14;PMEAN=37.2;PSTD=1;QUAL=37.7;QSTD=1;SBF=0.59883;ODDRATIO=1.2159237372632;MQ=60;SN=64;HIAF=0.0164;ADJAF=0;SHIFT3=14;MSI=2;MSILEN=1;NM=0.1;HICNT=32;HICOV=1946;LSEQ=GCGTACCCTTGTCCCCAGGA;RSEQ=GCATACGTGATGGCTGGTGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:2012:32:1975,32:0.0159:1015,960:18,14
the insert sequence "GCATACGTGATG" is a duplication of chr17:39724728 - 39724740. Thus I think the genomic location shoud be chr17: 39724740 not chr17: 39724742 with -3 parameter.
cmd: with -3
/Data/userhome/miniconda3/bin/vardict-java \ -3 \ ##the only difference -Q 15 \ -q 20 \ -th 10 \ -k 0 \ -G $ref \ -f 0.01 \ -N $sample \ -b ${sample}.rmdup.sort.bam \ -c 1 \ -S 2 \ -E 3 \ -g 4 \ -z 1 \ $bed \ |tee ${sample}.vardict.tbl \ |/Data/userhome/Biosoftware/VarDict/VarDictJava/VarDict/teststrandbias.R \ |/Data/userhome/Biosoftware/VarDict/VarDictJava/VarDict/var2vcf_valid.pl \ -S \ -N $sample -E \ -f 0.01 \
waiting for reply, thanks