Is there an option to supply a bed file with particular regions for phasing ?

twolinin / longphase

GNU General Public License v3.0

98 stars 6 forks source link

Is there an option to supply a bed file with particular regions for phasing ? #31

Open ilivyatan opened 8 months ago

ilivyatan commented 8 months ago

Is there an option to specify regions for phasing rather than the entire genome? Or do I have to preprocess the BAM to specific regions?

twolinin commented 8 months ago

You can preprocess the BAM to specific regions.

ythuang0522 commented 8 months ago

No. We thought the speed is fast enough for chromosome phasing without the need for region sampling. You can either extract the alignments from the bam or variants from the vcf in your interested region by samtools/tabix.