GATK variant calling on multiple bam files

Question

[User000]

Hello,

I am trying to do variant calling using GATK on a list of several hundreds of bam files like this:

bob.dup.bam
smith.dup.bam
will.dup.bam

This is the command line:

java -jar /Tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar HaplotypeCaller -L chr1:1-2096 -R ref.fasta -I bam/bam_list --min-base-quality-score 20 -O output.out

I get this error:

A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
  reference contigs = [chr1, chr2, chr3, chr4, chrUn]
  reads contigs = []

However, if I run for a single bam file separately it works.

java -jar /Tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar HaplotypeCaller -L chr1:1-2096 -R ref.fasta -I bam/bob.dup.bam --min-base-quality-score 20 -O output.out

What is the problem and how to solve this?

[Ram]

At least one of the BAMs has incompatible contigs in its header. Look through the headers of each BAM to find the incompatible one(s).

[User000]

I checked the header, it is ok, also because when I run all of them a as single bam files all of them work (for now I am working with 5 files to check). I suspect it is not recognizing the list of bam files?

[Ram]

You're right, -I doesn't seem to take a file, just a string of BAM names. Try either a comma separated list of names or a glob (like *.bam).

[Pierre Lindenbaum]

I'm not sure the latest version of HC is able to read a '*.list' suffix (this would be a bug)

can you please try

(..) `awk '{printf(" -I %s ",$0);}'  bam/bam_list  ` (...)

instead of

(..) -I bam/bam_list  (...)

[User000]

Oh... I realised what was wrong after your answer Pierre.... my bam list file name was bam_list (which works just fine for freebayes and bcftools), but GATK wants bam.list... Now it seems working... a very stupid mistake and all my pipeline was not working for days... :)

[Ram]

All it took was changing the file name from bam_list to bam.list?

[User000]

yeah.... I am not sure this particularity is specified in the GATK documentation... or may be I was not careful enough..