Currently trying to convert some BAM files back to FASTQ to perform
alignment with known parameters. Everything seems to be working, but there
is a file being generated by samtools which I can find no documentation or
explanation of. Running the following command:
samtools fastq -0 ${fname}_other.fq.gz -1 ${fname}_1.fq.gz -2
${fname}_2.fq.gz -@ 10 ${i} --reference
../../reference/hg19/GRCh38.p12.fna.gz
For output files I'm getting:
fname_1.fq.gz
fname_2.fq.gz
fname_other.fq.gz
Which is what I expect. However, I am also getting
fname_soft.fastq.gz
Any ideas what this fourth file contains and/or why it's being generated?
>From the name, my first guess would be that it contains the soft-clipped
reads from the BAM file. If so, are the non-clipped reads also being placed
in the _1 and _2 files? As far as I can find, there is no mention of the
_soft file anywhere in the documentation (either for the fastq command or
any other command). Any insight would be greatly appreciated.
Sincerely,
Jason Kost
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