Changes between Initial Version and Version 2 of Ticket #1253


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Timestamp:
Jun 4, 2020, 2:54:01 PM (3 years ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1253 – Description

    initial v2  
    55Instead, we should use the name of the Alignment item.
    66
    7 Existing VCF files should be manually fixed (with help of some clever grep/sed/awk/... commands).
     7Existing VCF files should be manually fixed (with help of some clever grep/sed/awk/... commands). Basically we can do `sed 's/S0123456.l.r.m.c.lib/S0123456.l.r.m.c.lib.g.k2.a/'` to replace all library names (`S0123456.l.r.m.c.lib`) with alignment names (`S0123456.l.r.m.c.lib.g.k2.a`). The `variants-filtered.vcf` file is not compressed and this can be done in-place with the -i flag to sed. But the raw and annotated files are compressed with bgzip so we need to decompress and re-compress before and after and probably need to store the result in a temporary file before overwriting the original file.