Question: Do I have to realign from scratch?
gravatar for Kasthuri
2.9 years ago by
United States
Kasthuri260 wrote:

I am working with human genomes I downloaded from TCGA (all bam files). I wanted to run GATK DepthOfCoverage which complained that the contigs are not compatible. I think GATK recommends aligning from scratch. Is there an easier way around than aligning from scratch? I tried Picard's ReorderSam but it doesn't work as well. Is there any way (script) to just change the contigs info in a .bam file. Here is the error message- Thanks!!

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.
##### ERROR   reads contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605, hs37d5]
##### 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]
incompatible contigs gatk • 1.0k views
ADD COMMENTlink modified 2.9 years ago by genomax80k • written 2.9 years ago by Kasthuri260

The best would be to get the correct reference genome for GATK, the one which was used for the alignment.

ADD REPLYlink written 2.9 years ago by WouterDeCoster43k

faster: get the reference fasta that was used to map the reads.

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum127k
gravatar for venu
2.9 years ago by
venu6.4k wrote:

It seems the reference genome you are using for this task and the reference genome used for aligning the raw data is different (hg19 & hs37d5 respectively, if my guess is correct). You can add chr prefix to your BAM chromosomes but I doubt GATK will complain again about those extra contigs. Try with hs37d5 genome, I think it won't complain.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by venu6.4k

Moved to answer and marked accepted.

ADD REPLYlink written 2.9 years ago by WouterDeCoster43k

Yes, it is indeed hs37d5. Thank you so much, everyone!

ADD REPLYlink written 2.9 years ago by Kasthuri260
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