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VarDictJava not reporting EGFR variant, perl version does

See original GitHub issue

L861Q_chr7_55259523-55259525.zip

See difference between:

vardict.pl -G /path/to/hg19.fa -f 0.001 -N abc -c 1 -S 2 -E 3 -g 4 -b L861Q.bam -R chr7:55259523-55259525

and

vardict-java -G /path/to/hg19.fa -f 0.001 -N abc -c 1 -S 2 -E 3 -g 4 -b L861Q.bam -R chr7:55259523-55259525

Issue Analytics

State:
Created 6 years ago
Comments:10 (10 by maintainers)

Top GitHub Comments

1reaction

chapmanbcommented, Mar 21, 2018

Miika, thanks for spotting this. Polina – thanks for this detective work and identifying the underlying issue. Is it possible to have a random assignment of CIGAR trimming to the forward or reverse strands for overlaps so we don’t introduce apparent bias? There would still be some decrease in frequency relative to consensus building, but it would resolve the most apparent change.

(while I’m writing, looks like Miika had a similar idea with R1/R2 based “randomization”)

0reactions

PolinaBevadcommented, Sep 6, 2018

@mjafin, thanks, I close the issue.

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