output conversion to SAM/BAM file
Closed this issue · 7 comments
Hi there,
I have a polyploid genome that I want to map to a haploid reference and want to calculate the depth/number of contigs aligning at each region. Is there a way to convert your output tsv file into a SAM file in order so simplify this?
Thanks!
I am assuming your input to this was a fasta file , can you not just align that using something like minimap2 ?
Yes it is a fasta file for the query assembly
I have already done it with minimap2 using the asm5 option
I was wondering if MashMap would perform differently, particularly in repetitive regions
Genome wide alignments is exactly what I want, its just I can have 3-4 phased haplotypes assembled within a single polyploid genome. Plus with the default 'map' filter I should have the best position of all query contigs.
Yes, this may be the case, the SAM is not the best format for these genome wide alignments, it's purely that there are already simple pipelines in place for coverage analysis using SAM/BAM files so I was hoping to take advantage of this
Thanks for the help
Updating this issue for MashMap v3
The new version of mashmap outputs a PAF file. Unfortunately, there are no plans at the moment for paftools.js
to support conversion from PAF to SAM/BAM.