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mattions/handycommands.md

Created September 21, 2015 10:04
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handycommands.md

Handy commands

Extract bam according to a bed file

bedtools intersect -abam path/to/input.bam -b path/to/regions.bed > out.bam

Extract region of a VCF

vcftools --gzvcf /archive/runs/BSset1_bwamem_freebayes/ILL1EX1G6/S1/aln/freebayes_prim.vcf.gz --chr 6 --out fb_test --from-bp 29910200 --to-bp 29920000 --recode --recode-INFO-all

Missing out the --recode-INFO-all will remove all of the info from the filtered file

Extract bed regions of a VCF

vcftools --gzvcf /archive/runs/BSset1_bwamem_freebayes/ILL1EX1G6/S1/aln/freebayes_prim.vcf.gz --bed example.bed --out fb_test --recode --recode-INFO-all

CAUTION: This seems to miss the first line of a bed file! Maybe it expects a header.

Pandas shortcut

if you have big dataframes, with a lot of columns, just writing:

import pandas as pd
pd.options.display.width = 180

and than you can see all your column in one line (handy if your script is big)

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