Difference between bcftools view and bcftools call?

Question

[AP]

Hi all,

This post is related to a previous one I wrote yesterday. Would anyone be able to tell me what is the difference between bcftools view and bcftools call?

My understanding is that bcftools call is the new view for bcftools versions 1.2 and above (I am using 1.3). However, it seems that filter options from view are not compatible with call (while I thought some would).

For instance, I am trying to use the -g filter options from bcftools view with call by typing the following but without success:

bcftools call -v -c -g hom|het|miss output.bcf > output.vcf

Alternatively, doing the following does not work either:

bcftools view -v -c -g hom|het|miss output.bcf > output.vcf

Is it possible to use the -g filter option from view with call? Any thoughts would be much appreciated!

Answer 1

[AP]

13 months later:

Using bcftools view should work although view was replaced by call in recent versions of bcftools (1.2 and 1.3). The -g filter option triggers an error probably due to a conflict between versions. Using bcftools call just does the job. Otherwise you need to go back to older versions.