Question: variant calling by GATK question about alignment
0
gravatar for rob.costa1234
17 months ago by
rob.costa1234150
United States
rob.costa1234150 wrote:

I have a human whole genome sequence data and I would like to call SNPs/ Indels/ mutations using GATK best practice module. Can I use Bowtie 2 for alignment. Which particular genome I have to use, Does GATK work with GRCH38 or hg19. I have tried to use hg19 as reference genome and GATK gave and error that Bam file does not have right header.

Thanks

alignment gatk • 533 views
ADD COMMENTlink modified 17 months ago by ijaz786besanttech0 • written 17 months ago by rob.costa1234150

Hello,

I have tried to use hg19 as reference genome and GATK gave and error that Bam file does not have right header.

please provide us the complete error message and the output of samtools view -H yourbamfile.bam.

fin swimmer

ADD REPLYlink written 17 months ago by finswimmer11k
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