Error with the reference file for GATK DepthOfCoverage

[Lilach]

Hi,
I am trying to use GATK DepthOfCoverage for chrX exome.
I got the BAM files from the lab that ran the NGS and I don't have their human reference genome fasta file. So I tried to give my human genome fasta files as a reference, but I got the following error.
Is there a way to overcome it without getting their fasta file? (which I'm not sure I can get in a short time and this is urgent).
I need only to check only chrX reads, although it was aligned to the whole genome.

Thanks!

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR contig reads = chrM / 16569
##### ERROR contig reference = chrM / 16571.
##### ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chrM]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR ------------------------------------------------------------------------------------------

[Zaag]

https://code.google.com/p/vcfsorter/

should do the trick

[Lilach]

Hi Zaan,
Thank you for the answer, but as well as I know I should give the bam file as input to GATK DepthOfCoverage and not the vcf, since I want to know which targets were not covered (and targets can be highly covered but without variants).
my Bam file is already sorted. I guess the problem is because its header is different than the fasta file header, becuase the supplier used a different fasta file as a reference.
Is there any other idea?

[Lilach]

I can create a new reference human genome without chrM and the other contigs, only chr1-22. Is there a way to tell the GATK DepthOfCoverage to ignore chrM?

[Zaag]

No you have chrM in your reads, I would recommend you to download the hg19 reference (chromFa.tar.gz) from here:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/

[Lilach]

My reference genome is indeed from hg19 chromFa.tar.gz, and the chrM.fa file there is the 16571 version.

I found a solution, and I'm writing it here for the community.
The 16569 chrM fasta version can be downloaded from NCBI pubmed nucleotide: NC_012920

I solved all other problems by cat a new reference file with only the chromosomes.

Thank you, Zaag, for the help!