olavurmortensen

# Define phasing pipeline.
@include "_snpindel_phaser_nocall.mro"

# TODO:
# Zipped VCF or not?
# can the phased_possorted_bam.bam be used as "input", even though a different one is supposed to be supplied (_LINKED_READS_ALIGNER/MERGE_POS_BAM/fork0/files/pos_sorted_bam.bam)?

call _SNPINDEL_PHASER_NOCALL(
    variants = "/mnt/fargen/experiments/freebayes_call_phased_bam/FN000518.vcf.gz",
    sex = "male",

olavurmortensen

[    16.354] 
X.Org X Server 1.18.4
Release Date: 2016-07-19
[    16.354] X Protocol Version 11, Revision 0
[    16.354] Build Operating System: Linux 4.4.0-45-generic x86_64 Ubuntu
[    16.354] Current Operating System: Linux telda 4.8.0-56-generic #61~16.04.1-Ubuntu SMP Wed Jun 14 11:58:22 UTC 2017 x86_64
[    16.354] Kernel command line: BOOT_IMAGE=/vmlinuz-4.8.0-56-generic.efi.signed root=/dev/mapper/ubuntu--vg-root ro quiet splash vt.handoff=7
[    16.354] Build Date: 02 November 2016  10:06:10PM
[    16.354] xorg-server 2:1.18.4-0ubuntu0.2 (For technical support please see http://www.ubuntu.com/support) 
[    16.354] Current version of pixman: 0.33.6

olavurmortensen

Notes

TODO:

1. Stuff
2. Other stuff
3. More stuff

olavurmortensen

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