Understanding bcftools command
1
0
Entering edit mode
10 weeks ago
rtho ▴ 20

I need to perform the following action to combine multiple vcf files into one

BCF=/path_to_bcftools
export BCFTOOLS_PLUGINS=$BCF/plugins
DIR=/path_to_normal_vcf_file
$BCF/bcftools merge -m all -f PASS,. --force-samples $DIR/*.vcf.gz |\
$BCF/bcftools plugin fill-AN-AC |\
$BCF/bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf

I don't have access to command-line bcftools, and since this is a one-time need I plan to use https://usegalaxy.org/ BUT I'm not clear how to implement the last two steps i.e.

$BCF/bcftools plugin fill-AN-AC |\
$BCF/bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf

Can I perform this entire command using Galaxy, and if so, can anyone guide me on how to carry out the last two lines?

Thank you

bcftools filter merge offtopic • 292 views
ADD COMMENT
0
Entering edit mode

This post does not fit the theme of this forum. Galaxy related questions belong on the galaxy help site: https://help.galaxyproject.org/

ADD REPLY
0
Entering edit mode

Please do not delete posts that have been answered.

ADD REPLY
0
Entering edit mode
10 weeks ago

If you look at the BCF tools in Galaxy you will see that each that you list can be run, and can be filled in with the appropriate parameters.

ADD COMMENT

Login before adding your answer.

Traffic: 1776 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6