No output from Samtools pileup

pravee1216 · 02-08-2011, 01:21 AM

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

ekg · 12-05-2012, 03:59 AM

Some tests I just did show that samtools mpileup only works for proper pairs. Can anyone else confirm this?

I was not able to call any variants until I marked the pairs with bamtools resolve.

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02-08-2011, 01:21 AM	#1
pravee1216 Member Location: India Join Date: Aug 2010 Posts: 35	No output from Samtools pileup 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

12-05-2012, 03:59 AM	#2
ekg Member Location: Boston, MA Join Date: Apr 2010 Posts: 36	Some tests I just did show that samtools mpileup only works for proper pairs. Can anyone else confirm this? I was not able to call any variants until I marked the pairs with bamtools resolve.