Hi, I've been given some BAM files (nothing else) and I'd like to call variants on them. I want to realign the sequences so I've been following the bam aln parameters:
bwa aln ref.fa -b1 reads.bam > 1.sai
bwa aln ref.fa -b2 reads.bam > 2.sai
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
The sampe stage is taking a *very* long time and with massive insert sizes suggesting the ordering is wrong. The bam files are sorted by read names, any suggestions on how I can make sure that 1.sai and 2.sai are ordered properly for the sampe stage to work, thanks.
bwa aln ref.fa -b1 reads.bam > 1.sai
bwa aln ref.fa -b2 reads.bam > 2.sai
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
The sampe stage is taking a *very* long time and with massive insert sizes suggesting the ordering is wrong. The bam files are sorted by read names, any suggestions on how I can make sure that 1.sai and 2.sai are ordered properly for the sampe stage to work, thanks.
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