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Depth is larger than AltDepth, strange variant #160

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worker000000 opened this issue Jun 8, 2021 · 0 comments
Open

Depth is larger than AltDepth, strange variant #160

worker000000 opened this issue Jun 8, 2021 · 0 comments

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@worker000000
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Dear professor,
Thanks for building such a poweful software, I found a strange variant using vardcit, the Depth is larger than AltDepth, and the deletion length is 471bp, really very large

this is my command

VarDict -G hg19_chr.fa -f 0.001 -N test -b test.bam -c 1 -S 2 -E 3 -r 2 -Q 30 -U -h test.bed >test.vardict.txt

perl vardict2vcf.pl test.vardict.txt test.vardict.vcf

chr7 140500846 . TACAAAATAGCTAACAGAATCAGACTACCTGATCTGTGGTACAAAATCATAATGCTTAATTTAATTGAAACAACTCTCCCTCTCCTCCTAGAAACTATCCAAAAATGGTTTCTATGGGTTAGGGGTCTTGATTAATTAAACGATAATATAAAATATAAATTAACTGTATAGCTGAACCAGCATTACAATTTGGGAGAGAAATACTGTCCATTCCACATATTATTCTCTAACTACACTTAAAAAAAATTCTCTATAACAATCGTATGGAAGAAAAACCCTCACAGACTTTTAGACATCGTAGCTTCACATTAAGAAAATTTAAGTGTAAAATGGTAGGTAGAAAAGAGATATTTTTGGATTACTTACTCAAGTTGGTCATAATTAACACACATCAGTGGAACTTCTGTACTACAACGCTGGTGAAATTTATAACCACATGTTTGACAGCGGAAACCCTGGAAAAGCAGCTTTCG T . . . GT A/-472 1 4 1.0000

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