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Old 04-10-2012, 04:17 PM   #1
ramirob
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Location: Vermont

Join Date: Apr 2012
Posts: 14
Default Samtools on Chromosomes Versus Genome

Hi everyone,

Does anybody have experience running samtools on CASAVA alignments?

I am trying to call SNPs using samtools on a CASAVA/illumina alignment.

CASAVA outputs an alignment of the type name_export.txt.gz

and it automatically converts to BAM format when using their SNP caller.

Now I want to call SNPs using Samtools.

The alignment was done using each chromosome individually:

genomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/Chr...

However, the BAM alignment provided by CASAVA is for the whole genome, so then should I use the whole reference genome?:

samtools mpileup -f ../genomes/Homo_sapiens/UCSC/hg18/Sequence/WholeGenomeFasta/genome.fa sorted.bam > sorted.mpileupOutput

the problem is that, in that case the mpileup output doesn't seem to recognize it as I get:

bash-3.2$ head -n 100 sorted.mpileupOutput
chr1.fa 3309 N 1 ^NT C
chr1.fa 3310 N 1 G C
chr1.fa 3311 N 1 C F
chr1.fa 3312 N 1 C F
chr1.fa 3313 N 1 C F


Any ideas??

Thanks in advance,

Ramiro
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