Question: RealignerTargetCreator (GATK) contig issue
0
gravatar for win
18 months ago by
win810
India
win810 wrote:

So i downloaded a .bam from phase 3 1000 genomes and i want to run the RealignerTargetCreator on it using GATK 3.8.

The following command works fine:

sudo java -jar algorithms/gatk/gatk3.8.jar -T RealignerTargetCreator -R references/hg38.fasta -I data/HG100.reordered.bam -o data/HG100.realignertargetcreator.intervals

But when this command is run with -know i get contigs mismatch error between my bam and the vcf file. The know indel VCF used is located here:

https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz

Step prior I have applied the picard ReorderSam using hg38.

Am i using the incorrect indels file?

Thanks in advance.

gatk • 822 views
ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum121k • written 18 months ago by win810
0
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

check the names, the length and the order of the contigs in

$ wget -q -O - "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" | gunzip -c | grep '##contig'

is the same as

$ samtools view -H data/HG100.reordered.bam | grep '^@SQ'
ADD COMMENTlink written 18 months ago by Pierre Lindenbaum121k

Thanks, in the know_indels.vcf.gz i can see a lot of HLA-A, HLA-B, HLA-C contigs, where is not in the reordered BAM. Can this be an issue?

ADD REPLYlink written 18 months ago by win810

i can see a lot of HLA-A, HLA-B, HLA-C contigs, where is not in the reordered BAM. Can this be an issue?

yes

ADD REPLYlink written 18 months ago by Pierre Lindenbaum121k

........and how do take care of this issue?

ADD REPLYlink written 18 months ago by win810

change the sequence dictionary in the bam (insert the missing lines using samtools reheader ) or remove the ##contig lines and the variants in the vcf.

ADD REPLYlink written 18 months ago by Pierre Lindenbaum121k

OK, will try. I have never done any of this before.

ADD REPLYlink written 18 months ago by win810

Consider @Devon's instructions as you try samtools reheader: A: Problems while reheadering BAM with Samtools 1.3.1

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax70k
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