Hi All,
I have been struggling with an issue where mpileup refuses to work find variation in a given bamfile. In fact, when using the standard mpileup routine described on the samtools website, the vcf file contains only 11 'SNPs', all of which are filtered out by the default conditions in vcfutils.pl step. This is a pooled sample from multiple unrelated individuals (birds), so I know that there is variation.
Anyway, I had been using Bowtie2, but on a whim, tried Bowtie1, and like magic, now there are 10K SNP's, which is a reasonable number for my study design.
So, I am wondering, what is it about Bowtie2 that mpileup does not like?
Here is a SAM entry for a read in bowtie2
Here is the same read in bowtie1
What do you guys think? Is this a SAM format issue, a bug in mpileup, something else?
I have been struggling with an issue where mpileup refuses to work find variation in a given bamfile. In fact, when using the standard mpileup routine described on the samtools website, the vcf file contains only 11 'SNPs', all of which are filtered out by the default conditions in vcfutils.pl step. This is a pooled sample from multiple unrelated individuals (birds), so I know that there is variation.
Anyway, I had been using Bowtie2, but on a whim, tried Bowtie1, and like magic, now there are 10K SNP's, which is a reasonable number for my study design.
So, I am wondering, what is it about Bowtie2 that mpileup does not like?
Here is a SAM entry for a read in bowtie2
Code:
HS2:124:C097KACXX:7:2307:12782:66337 113 4 2 42 98M 396128 3022 0 AGCTCCAGCCATTCCCTGGGGGCTGTCCCTGATCATCACAGCCTCTCTGGCCACCCTGGGCTGAGCACGGTGTCTGAGTCTGCTTTGACCCAGGACCA BC??BBCB@A?BBBBB@BBBBBBCBBECCDEDDD?EC?FEHIIIIIIGIGIGBIHGDGFIIIIHGFDGEGIIIIIIHGFIGHAHGCCAGHFEDDD@@@ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:98 YS:i:0 YT:Z:DP
Code:
HS2:124:C097KACXX:7:2307:12782:66337 16 4 2 255 98M * 0 0 AGCTCCAGCCATTCCCTGGGGGCTGTCCCTGATCATCACAGCCTCTCTGGCCACCCTGGGCTGAGCACGGTGTCTGAGTCTGCTTTGACCCAGGACCA BC??BBCB@A?BBBBB@BBBBBBCBBECCDEDDD?EC?FEHIIIIIIGIGIGBIHGDGFIIIIHGFDGEGIIIIIIHGFIGHAHGCCAGHFEDDD@@@ XA:i:0 MD:Z:98 NM:i:0
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