Look into freebayes. There is samtools/bcftools based option as well.
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sorted bam and bbmap
Is there an option for bbmap that will result in a sorted bam? I know adding "out=mapped.bam" this will produce a bam but it appears to be unsorted:
Code:samtools view -H /home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam @HD VN:1.4 SO:unsorted
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Originally posted by GenoMax View PostNo. You have to do some work
Code:$ samtools sort your_file.bam your_file_sorted
Code:bbmap.sh in=reads.fq out=mapped.bam bs=bs.sh; sh bs.sh
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Originally posted by westerman View PostCouldn't you create the shell script and then execute it within BBMap?
It would work fine on most individual computers since physical memory limits would never be exceeded, but job schedulers often have strict limits on virtual memory and will kill jobs that exceed it. So, it would reduce stability (and typically fail) on clusters unless I did parsing in the shellscript to launch a new process after BBMap terminates, or the user launched BBMap with a custom -Xmx flag. I try to keep the shellscripts as simple as possible. Anyway, there are workarounds, but they all add complexity due to memory issues.
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