I tried to call consensus using samtools pileup from the filtered BAM file which has only reads with no mate. But the result was empty. The following is what I did:
1) From the complete BAM, I extracted reads (mapQV >8) which have no mate (mate unmapped) using "samtools view -f 0x8" - There are ~35m reads.
2) removed all duplicate reads using Picard
3) provided this filtered file to samtools for consensus calling with options "-c", "-Q 8", "-f ref.fas" ( i tried -m, -M as well)
Question here is 1) Why does pileup fail to call consensus 2) Did i make any mistake or do I modify any parameters 3) Is there any other tool can do this?
Any light to this will be a great help.
Thanks.
Praveen
1) From the complete BAM, I extracted reads (mapQV >8) which have no mate (mate unmapped) using "samtools view -f 0x8" - There are ~35m reads.
2) removed all duplicate reads using Picard
3) provided this filtered file to samtools for consensus calling with options "-c", "-Q 8", "-f ref.fas" ( i tried -m, -M as well)
Question here is 1) Why does pileup fail to call consensus 2) Did i make any mistake or do I modify any parameters 3) Is there any other tool can do this?
Any light to this will be a great help.
Thanks.
Praveen
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