Hi,
I am trying to wrangle samtools into giving me a consensus, using reads mapped with bwa to a reference. After I generate a BAM, the results look pretty good using samtools tview:
So, there is good coverage, etc.
Now, when I try to generat a consensus, for example, by
I get a whole lot of Ns in my consensus
I swear, I tried every combination of samtools and bcftools I could think of. Adding a reference sequence also doesn't make any difference. Any ideas would be most very much appreciated.
Sasha
I am trying to wrangle samtools into giving me a consensus, using reads mapped with bwa to a reference. After I generate a BAM, the results look pretty good using samtools tview:
So, there is good coverage, etc.
Now, when I try to generat a consensus, for example, by
Code:
samtools pileup -6Aug sorted.bam |bcftools view -cg - | vcfutils.pl vcf2fq
Code:
@gi|159883886|emb|CU329670.1| nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnn + !!!!@@@@@@@@@@CEEEHHHHHHHHHHHHHHNKKNKQQQWWWWWWccux{{{{{~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~
Sasha
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