Error while running vcf2maf tool
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12 months ago
Jordan ★ 1.2k

Hi,

I'm running vcf2maf.pl on about 100 VCF files. But some files (about 10) do not report any MAF, and they report the below error:

Can't exec "/bin/sh": Argument list too long at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376.
Use of uninitialized value in concatenation (.) or string at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376.
Can't exec "/bin/sh": Argument list too long at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376.
Use of uninitialized value in concatenation (.) or string at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376.
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 390.

Here is the code I used for running:

vcf2maf.pl --input-vcf $somatic_vcfs/${file_base%.vcf.gz}.somatic.vcf\
                --output-maf $maf_out/${sample}.maf \
                --tumor-id $tumor_id \
                --normal-id $normal_id \
                --species homo_sapiens \
                --ncbi-build GRCh38 \
                --cache-version 96 \
                --ref-fasta $ref \
                --vep-forks 14 \
                --vep-path $vep_path \
                --vep-data $vep_data

I'm unsure why this error happens only for a select VCF files.

Any help is appreciated!

vep vcf2maf variant-calling vcfs maf • 496 views
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use the ${variable} syntax in all your variables to avoid expansion.

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Can you search for the error and try some of the suggested solutions? - it has been reported previously. The error is:

ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.

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