GATK HC mis-reading chromosomes

Question

[Ace]

My command:

$GATK HaplotypeCaller -R $ref -L $locations -I Bamfiles.txt -ploidy 1

The user error looks like this:

A USER ERROR has occurred:
Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [All of the correct contigs are listed out]
reads contigs = []

Meaning, the reads contigs are being read-in as blank

I thought maybe one of my files was aligned incorrectly. I looked at their headers

for file in $(cat Bamfiles.txt); do samtools view -H $file; done | sort | uniq -c > Out.txt

The counts for each chromosomal header were consistent and the same numbers as I have samples. The only thing that looked different: about 1/4 of my samples (from an earlier study) had VN (sam version): 1.3 while the rest had VN: 1.5. Could this be enough to cause GATK to reject my samples and if so is there an easy way to convert between samfile 1.3 and 1.5 or should I re-align them?

[Ace]

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[GenoMax]

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Answer 1

[Ace]

Update: I've fixed the error, and boy do I feel silly. I totally forgot how essential it is to have your bamfile list end in ".list". Poor GATK was reading my list as a bam file; no wonder it couldn't find any chromosomes! Closing the question now, thanks for your help!

Answer 2

[Pierre Lindenbaum]

the sequence dictionaries (lines in the bam headers starting with @SQ and the lines in the .dict file) are not the same.

and looking at reads contigs = [] , i wonder if there is any dict in your bam files ?

[Ace]

Right, so when I looked at this initially my first step was checking that the headers in the bam file were right. Indeed, each line looks something like this @SQ SN:$chromosome LN:$length and the chromosomes correspond correctly to the chromosome in the reference fasta.

I thought it might be an error with a missing index, so I tried re-indexing all of them with

 for file in $(cat $Bamfiles); do echo $file; samtools index $file; done

Unfortunately, this alone did not fix the error. Is there a way to check their content?