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Filter variants supported by 20% of total reads

Hi All

How can I get all variants (.vcf) found in ≤20% of total reads in .bam?

Explanation :

  1. Single-End RNAseq, I have STAR 2-pass aligned .bam files (several samples).

  2. Competed Marked duplicates & sort (Picard), and SplitNCigarReads, BaseRecalibration (GATK)

  3. I generated .vcf (samtool mpileup and BCFTools call) containing number of reads supporting a variant (DP=raw_depth, AD=Total Allelic depth).

My aim is to:

A:get variant.vcf present in ≤20% of total reads in .bam file.

B: detect rare variants.

Is there any program or script available ?

Thanks in advance.

snp rna-seq alignment sequence
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Ks-seq • Ks-seq

Your data is from an RNA-seq experiment, but you are calling variants with SAMtools...?

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written by Kevin Blighe Kevin Blighe

Thanks for your comment, Yes, I want to detect rare variant so I want to see everything before any filtering. Therefore, samtools mpileup will give me everything (i think so, if not then please c) And then correct me). Thereafter, I want to study variant present in ≤20% of total reads. Basically, I want get all variants found in ≤20% of total reads in .bam file.

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written by Ks-seq • Ks-seq

You could probably do this manually via mpileup output and even combinations of cut, uniq -c, and awk. There are likely many ways.

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written by Kevin Blighe Kevin Blighe

Could you please guide me with an example? THis is how my vcf looks lke:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Y.bam

Y 5325732 . T G,<*> 0 . DP=1;ADF=0,1,0;ADR=0,0,0;AD=0,1,0;I16=0,0,1,0,0,0,0,0,0,0,20,400,0,0,1,1;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL:DP:SP:ADF:ADR:AD 4,3,0,4,3,4:1:0:0,1,0:0,0,0:0,1,0

Y 5325733 . T G,<*> 0 . DP=1;ADF=0,1,0;ADR=0,0,0;AD=0,1,0;I16=0,0,1,0,0,0,0,0,0,0,20,400,0,0,2,4;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL:DP:SP:ADF:ADR:AD 4,3,0,4,3,4:1:0:0,1,0:0,0,0:0,1,0

Y 5325734 . A G,<*> 0 . DP=1;ADF=0,1,0;ADR=0,0,0;AD=0,1,0;I16=0,0,1,0,0,0,0,0,0,0,20,400,0,0,3,9;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL:DP:SP:ADF:ADR:AD 4,3,0,4,3,4:1:0:0,1,0:0,0,0:0,1,0

Y 5325735 . T C,<*> 0 . DP=1;ADF=0,1,0;ADR=0,0,0;AD=0,1,0;I16=0,0,1,0,0,0,0,0,0,0,20,400,0,0,4,16;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL:DP:SP:ADF:ADR:AD 4,3,0,4,3,4:1:0:0,1,0:0,0,0:0,1,0

Y 5325736 . G A,<*> 0 . DP=1;ADF=0,1,0;ADR=0,0,0;AD=0,1,0;I16=0,0,1,0,0,0,0,0,0,0,20,400,0,0,5,25;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL:DP:SP:ADF:ADR:AD 4,3,0,4,3,4:1:0:0,1,0:0,0,0:0,1,0

I tried samtools mpileup and bcftools mpileup and bcftools call but cant get anything out. Appreciating you much for your help.

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written by Ks-seq • Ks-seq

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