Question: variant calling by GATK question about alignment
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gravatar for rob.costa1234
2.2 years ago by
rob.costa1234190
United States
rob.costa1234190 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 • 745 views
ADD COMMENTlink modified 2.2 years ago by ijaz786besanttech0 • written 2.2 years ago by rob.costa1234190

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 2.2 years ago by finswimmer13k
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