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Non-reproducible variants called with same command for vardict #390

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KshamaGoyal opened this issue Jun 7, 2023 · 0 comments
Open

Non-reproducible variants called with same command for vardict #390

KshamaGoyal opened this issue Jun 7, 2023 · 0 comments

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@KshamaGoyal
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I used the following vardict command:

/usr/local/bin/vardict -G hg38_genome.fasta -f 0.01 -N DNA_VT_run1 -b DNA_VT_run1.bam -c 1 -S 2 -E 3 -g 4 -r 2 my_target_bed_23mar2023.bed| /usr/local/bin/teststrandbias.R | /usr/local/bin/var2vcf_valid.pl -N sample_name -E -f 0.01 > DNA_VT_run1_job3_minRead3.vcf

I executed the same command 3 times and got different variant list.

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@KshamaGoyal