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how to filter using vcf from multiple samples generated by mpileup2somatic

Status: Open.

#67 In dkoboldt/varscan;

· weiydcn opened on Feb 19, 2024

varscan2 output can't be fed to snpEff. ID column missing?

Status: Open.

#66 In dkoboldt/varscan;

· gabrielet opened on Feb 2, 2024

Why genotype and depth representations are inconsistent

Status: Open.

#65 In dkoboldt/varscan;

· fjptwenger opened on Jun 15, 2023

filter for pielup2cns not working

Status: Open.

#64 In dkoboldt/varscan;

· zoeward-nz opened on Jan 9, 2023

two mutations on one pos can't call out

Status: Open.

#63 In dkoboldt/varscan;

· user-tq opened on Feb 16, 2022

log4j

Status: Open.

#62 In dkoboldt/varscan;

· myourshaw opened on Jan 26, 2022

Reads supporting a variant

Status: Open.

#61 In dkoboldt/varscan;

· biounix opened on Mar 22, 2021

How to pipe deovo trio with samtool mpileup?

Status: Open.

#59 In dkoboldt/varscan;

· snijesh opened on Jan 13, 2021

Not filtering reverse strand's strand bias

Status: Open.

#57 In dkoboldt/varscan;

· svarona opened on Nov 25, 2020

mpileup2snp do not detect all snps

Status: Open.

#56 In dkoboldt/varscan;

· wwang-chcn opened on Sep 25, 2020

NumberFormatException in varscan somatic

Status: Open.

#55 In dkoboldt/varscan;

· Jasondai9 opened on Sep 22, 2020

Malformed VCF output

Status: Open.

#54 In dkoboldt/varscan;

· jfnavarro opened on Jul 21, 2020