Do I have to realign from scratch?

Question

[Kasthuri]

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]

[WouterDeCoster]

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

[Pierre Lindenbaum]

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

Answer 1

[venu]

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.

[WouterDeCoster]

Moved to answer and marked accepted.

[Kasthuri]

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