Question: RNA-seq snp discovery use bcftools
0
gravatar for mra8187
24 days ago by
mra818720
mra818720 wrote:

dear all i using this script for my work but i get error

bcftools view -N -I -l snp_list.txt accepted_hits_re_mpileup_out.txt > accepted.bcf

error :

view: invalid option -- 'N'

i know that this option is not in the list of bcftools and so get this error... i try all version of bcftoos ... 1.11 to 1.10 1.9 ......1.1 but i cant find the versin that has "-N" options

snp rna-seq bcftools • 108 views
ADD COMMENTlink modified 24 days ago by GenoMax95k • written 24 days ago by mra818720

The option does not exist. What would you like to trigger with it, so which option or output do you need?

ADD REPLYlink modified 24 days ago • written 24 days ago by ATpoint44k
2
gravatar for Istvan Albert
24 days ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

The valid flags for bcftoools view can be seen here

http://samtools.github.io/bcftools/bcftools.html#view

the command as listed seems to be incorrect (or extremely out of date and not something you should pursue), that's the simple explanation.

Perhaps it should've lower case n, -n for novel.

You also list -l with no compression level specified, and the input file seems to be a text pileup file,

all that indicates an outdated usage. Today the command to turn pileups into variants is bcftools call

so rework that command to be correct.

ADD COMMENTlink written 24 days ago by Istvan Albert ♦♦ 86k

thank you for your answer so which work flow you suggest to me for allele specific expression? thank you

ADD REPLYlink written 24 days ago by mra818720
1

bcftools is a software that (among the many features) allows you to generate and filter variants.

The process you have to follow is not running someone else's code that you don't understand. Instead study that code, understand what it does, then apply the parameters yourself.

In your case run bcftools call followed by bcftools view with some extra parameters will select a subset of variants.

When it comes to allele-specific expression, that is a completely different question, it is unrelated to bcftools you need to ask that separately. This thread is really about how to run bcftools. We like to keep related content in a single thread.

ADD REPLYlink written 23 days ago by Istvan Albert ♦♦ 86k
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