varscan2 mpileup2snp output contains indels
Hi all,
I ran varscan2 mpileup2snp but I see that the vcf output file contains indels?
Record(CHROM=TR1087|c2_g1_i4, POS=1195, REF=TAAAAAAAAA, ALT=[AAAAAAAAAA, TA, T, TAAAA, TAAA, TAA, T]) Record(CHROM=TR669|c3_g1_i3, POS=3524, REF=CAAAA, ALT=[C, AAAAA, C, CAAAAA, C]) Record(CHROM=TR361|c2_g1_i1, POS=268, REF=A, ALT=[T, AA, AAAA, AAAAT, AAA])
varscan/2.3.9/varscan mpileup2snp file.pileup --min-coverage 2 --min-reads2 2 --min-avg-qual 20 --min-var-freq 0.01 --min-freq-for-hom 0.85 --p-value 1 --strand-filter 1 --output-vcf 1 --vcf-sample-list vcf-sample-list.txt > file.mpileup.mpileup2snp.vcf
How I do remove these indels?
Thanks for your help!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Issue with VCF format while using Pharmcat
written by taniamahmood38 •
-
Not returning any alleles when using bcftools view -q
written by kshaffman •
-
iadmix - population stratification for Genotype data
written by samreen.jasvi •
-
Problem understanding GT from Varscan's vcf output
written by ww22runner •
-
VarScan.v2.3.9 filter error p-value
written by niggoK •
-
varscan somaticFilter thinks all my variants are near INDELS so removes all of them
written by wes3985 •
-
Varscan variant calll error on pacbio data
written by mark.rose •
-
Questions In Output Of Varscan 2.3.2
written by rahilsethi •
-
Best Way To Compare Output Snp/Indels From Different Software?
written by Hmm •
hi, I too use mpileup2snp (ver. 2.3.6) for single-sample calling but haven't observed what you are showing. In any case, this GATK utility can parse out SNPs/ InDels from a VCF.