Timeline for How to subset a BAM by a list of QNAMEs?
Current License: CC BY-SA 3.0
5 events
| when toggle format | what | by | license | comment | |
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| Oct 24, 2022 at 9:28 | comment | added | bepoli | As it was already said, this is very slow. You can easily do this much faster with samtools or picard (see mine or Pierre's answers). | |
| Sep 25, 2019 at 7:52 | comment | added | wjv |
Since the qnames are all fixed strings, using fgrep instead of grep will provide a significant speedup — several orders of magnitude. However, both approaches may lead to spurious results: If you have a qname foo in our list, and the BAM file also contains qnames fooX and fooY, the latter will also be returned in your results, erroneously.
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| Dec 11, 2018 at 22:10 | comment | added | conchoecia | This is quite slow if the bam file or the list of reads to keep are of appreciable size. | |
| Jan 25, 2018 at 18:19 | vote | accept | EB2127 | ||
| Jan 23, 2018 at 18:49 | history | answered | Bioathlete | CC BY-SA 3.0 |