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r3fang / SnapTools

A module for working with snap files in Python
Apache License 2.0
35 stars 21 forks source link

bam file to the snap format? #1

Open shawnzhangyx opened 5 years ago

shawnzhangyx commented 5 years ago

Hi Rongxin,

Thanks for making this great tool! With Snaptools, I wondering if there is option to start with the bam files, rather than fastq? For example, if I already performed the alignment, can I feed the bam files to the program and get the snap files?

r3fang commented 5 years ago

Yes, just skip the first two steps and start with ‘snaptools pre’ with unfiltered bam or bed as input. Bam or bed file needs to be sorted by read name before running this step.