convert PAF to SAM#493 New issue Closed pterzian Hi, I have a bunch of PAF files that I would like to use withsamtools mpileupto recover the read coverage for a given a list of genomic position. *Those PAFs are
out of the box. However, many conversions require external tools. This is why we recommend to use acondaenvironment. In particular, most external tools are available on thebiocondachannel. For instance if you want to convert a SAM file to a BAM file you would need to installsamtoolsas ...
Then, concatenate the output of a command like this:: parallel-fastq "... | maf-convert.py -n sam" < q.fastq * Here is yet another way to get a sequence dictionary, using samtools (http://samtools.sourceforge.net/). Assume the reference sequences are in ref.f...