varscan2 mpileup2snp output contains indels

Question

[AW]

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!

[Amitm]

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.