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
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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