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