RNA-seq snp discovery use bcftools

Question

[mra8187]

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

[ATpoint]

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

Answer 1

[Istvan Albert]

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the command as listed seems to be incorrect (or extremely out of date and not something you should pursue), that's the simple explanation.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all that indicates an outdated usage.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

[mra8187]

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

[Istvan Albert]

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.