How to add flags to callvariants.sh?

Question

[marongiu.luigi]

I would like to obtain a complete outlook for an alignment and a graph using callvariants.sh from the BBtools package. I understand that the flags needed are clearfilters and mhist but I don't understand how to set the flags properly.

I tried with

callvariants.sh in=<in>.sam.gz ref=<ref>.fa out=<out>_vars.vcf --clearfilters --mhist

and other combinations, but it does not work.

What is the correct syntax?

Thank you

Answer 1

[GenoMax]

Should be

callvariants.sh in=sam.gz ref=ref.fa out=out_vars.vcf clearfilters

There is no mhist option though.

$ callvariants.sh | grep hist
shist=<file>    (scorehist) Output for variant score histogram.
zhist=<file>    (zygosityhist) Output for zygosity histogram.
qhist=<file>    (qualityhist) Output for variant base quality histogram.

If you wanted to use one of these then you will do

callvariants.sh in=sam.gz ref=ref.fa out=out_vars.vcf qhist=filename clearfilters

[marongiu.luigi]

Thank you, now I see how to call the flags in callvariants.sh. However, how do I get an output such as in this post (Brian Bushnell's answer)? clearfilters did not add much more information and the *hist field are not images...