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
Jiarong
$ 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
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
Jiarong
$ 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