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Hello World!
I've just done a quick spot check comparing the simple pileup outfile between pileup and mpileup in samtools version 0.1.12a
What I noticed is that mpileup does not use reads for which the paired read maps to a different chromosome. A simple example is as follows
samtools pileup -s -f ......
chr10 50006 C 1 ^!. H !
chr10 50007 C 3 .^!.^!. HHH !!!
chr10 50008 T 3 ... HHH !!!
chr10 50009 T 4 ...^!. CHHD !!!!
chr10 50010 G 5 ....^!. HHHDH !!!!!
chr10 50011 A 5 ..... FFHDH !!!!!
chr10 50012 G 6 .....^!. HHHDHH !!!!!!
samtools mpileup -s -f ......
chr10 50007 C 2 ^!.^!. HH
chr10 50008 T 2 .. HH
chr10 50009 T 3 ..^!. HHD
chr10 50010 G 4 ...^!. HHDE
chr10 50011 A 4 .... FHDH
chr10 50012 G 5 ....^!. HHDHB
The read that begins at chr10:50006 appears to have a paired read on chromosome 18 although all 100 bases match with high mapping quality: Summarizing the read details:
chr10 50006 0 100M chr18 4496
I'm pretty new to the game and would like to know that your thoughts are on this, if it's a problem, better. I would think that this is perhaps throwing away data which could affect variant calling....
I've just done a quick spot check comparing the simple pileup outfile between pileup and mpileup in samtools version 0.1.12a
What I noticed is that mpileup does not use reads for which the paired read maps to a different chromosome. A simple example is as follows
samtools pileup -s -f ......
chr10 50006 C 1 ^!. H !
chr10 50007 C 3 .^!.^!. HHH !!!
chr10 50008 T 3 ... HHH !!!
chr10 50009 T 4 ...^!. CHHD !!!!
chr10 50010 G 5 ....^!. HHHDH !!!!!
chr10 50011 A 5 ..... FFHDH !!!!!
chr10 50012 G 6 .....^!. HHHDHH !!!!!!
samtools mpileup -s -f ......
chr10 50007 C 2 ^!.^!. HH
chr10 50008 T 2 .. HH
chr10 50009 T 3 ..^!. HHD
chr10 50010 G 4 ...^!. HHDE
chr10 50011 A 4 .... FHDH
chr10 50012 G 5 ....^!. HHDHB
The read that begins at chr10:50006 appears to have a paired read on chromosome 18 although all 100 bases match with high mapping quality: Summarizing the read details:
chr10 50006 0 100M chr18 4496
I'm pretty new to the game and would like to know that your thoughts are on this, if it's a problem, better. I would think that this is perhaps throwing away data which could affect variant calling....