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Old 08-10-2013, 08:20 PM   #1
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Location: USA

Join Date: Feb 2009
Posts: 1
Smile samtools mpile up problem

Hi all,

I have one reads mapped to a contig (merged-96) by bowtie2, but when I did "samtools mpileup" with the bam file, no per base coverage info is showed.

The flag "272" = 256 (the alignment is not primary) + 16 (reverse strand). "samtools mpileup" does not take secondary alignments? In my case, I want to coverage from secondary alignments. Any ideas? thanks


$ samtools view merged96.bowtie2.sorted.bam
2317:7:2304:17786:75275#TTAGGCA/2 272 merged-96 27 0 35M * 0 0 AATTCCGGCAGCTTGTATTCTTCGAGCCGGAACAG * AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:32T1A0 YT:Z:UU

$ samtools mpileup merged96.bowtie2.sorted.bam
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
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