Hi, we're using older version (1.6.17) of vcf2maf and recently it choked on a vcf with line (I zeroed out the exact locus)
13 32900000 NM_000059.3:c.0000-000_*1500000del G <DEL> . PASS;EXT "END=34400000;SVTYPE=DEL;SVLEN=1500000;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=C";ANN=<DEL>|upstream_gene_variant.....
Here are the error messages
Use of implicit split to @_ is deprecated at vcf2maf.pl line 1046.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 167.
[fai_fetch] Warning - Reference :- not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 167.
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 167.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
Use of uninitialized value in concatenation (.) or string at vcf2maf.pl line 289, <GEN0> line 171.
[fai_fetch] Warning - Reference :- not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 171.
Use of uninitialized value in join or string at vcf2maf.pl line 291, <GEN0> line 171.
Argument "" isn't numeric in subtraction (-) at vcf2maf.pl line 361, <GEN2> line 167.
Argument "" isn't numeric in subtraction (-) at vcf2maf.pl line 361, <GEN2> line 172.
[fai_fetch] Warning - Reference :-1-1 not found in FASTA file, returning empty sequence
Failed to fetch sequence in :-1-1
[tabix] failed to load the index file.
WARNING: Couldn't retrieve bps around :1 from reference FASTA: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
WARNING: Couldn't retrieve bps around :1 from reference FASTA: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
STATUS: Running VEP and writing to: /tmp/tmp.0iCZQthiPu/sample.vep.vcf
WARNING: Chromosome not found in annotation sources or synonyms on line 24
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 316, <$__ANONIO__> line 173.
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm line 412, <$__ANONIO__> line 173.
Argument "946047"" isn't numeric in abs at /mnt/datateamsftp/bin/vcf2maf/VEP/ensembl-vep-release-95.3/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 316, <$__ANONIO__> line 173.
The first warning seems to point to this code
# Fetch the REF allele at the second breakpoint using samtools faidx
my $ref2 = `$samtools faidx $ref_fasta $info{CHR2}:$info{END}-$info{END} | grep -v ^\\>`;
But it seems CHR2 is an optional term in INFO? Is that the problem or am I missing something? The exact line is still there now, btw
Hi, we're using older version (1.6.17) of vcf2maf and recently it choked on a vcf with line (I zeroed out the exact locus)
Here are the error messages
The first warning seems to point to this code
But it seems CHR2 is an optional term in INFO? Is that the problem or am I missing something? The exact line is still there now, btw