Option "Calmd" For Whole-Exome Is Very Confusing:

Question

[Angel]

Hello: I ran:

samtools calmd -Abr FOO.sorted.bam human_18.fasta > FOO.baq.bam

samtools index foo.baq.bam foo.bam.bai

How should I utilize "calmd" output as it is considered to give better quality SNPs? The following two commands are fine if I use input "foo.sorted.bam" instead of calmd output. WHen I use ".baq.bam" as input, I get empty files as outputs.

samtools mpileup -u hg19.fa foo.baq.bam | bcftools view - > foo.calmd.bcf

bcftools view food.calmd.bcf | vcfutils varFilter -D200 > foo.d200.flt.vcf

Please help thanks!

[Ashutosh Pandey]

I just realized that this is a pretty old question (2.4 years old) . I am sure that the user may not be waiting for the answer. I think there should be a time limit thing so that the unanswered questions that are too old don't appear. Its is so easy for a user like me or Andreas to not notice this thing and waste our time answering these questions. It has happened to me several times before I realized that the question was too old to answer. Most of these unanswered questions are error messages that were created because of the wrong command usage. It would be better if we can stop them to reappear. I am not against a genuine question that is too old but as i said most of these are either due to bug in the software that has been resolved or wrong command usage.

[Ashutosh Pandey]

BTW, I am not sure if the question appeared automatically or Andreas searched for this questions and answered it.

[Andreas]

Hi Ashutosh, I had searched the net for info about calmd usage and by chance came across this question. I didn't notice it was that old though. Not sure what to do with old unanswered questions in general.

Andreas

[Ashutosh Pandey]

Hi Andreas, Thanks for clarifying it. I thought some automation process in biostars keeps bringing the old unanswered questions.

[Devon Ryan]

The user Biostar does do that, in fact, when it retags things. Perhaps we should add it not doing that as a feature request.

Answer 1

[Andreas]

Hi Angel,

samtools' calmd command adds BAQ information to the BAM file which can then be used by downstream tools. samtools mpileup adds this information automatically on the fly, if it's not already in there. So in theory using calmd before mpileup or not using it, should produce identical results (unless the BAQ options for calmd and mpileup were set differently).

Having said this, I can only guess why you get empty results when using the calmd preprocessed file as opposed to the not preprocessed file. Is foo.calmd.bcf already empty? Are you sure the usage is correct (check against http://samtools.sourceforge.net/mpileup.shtml ). For example, I think you require -f before your fasta reference...

Andreas