Question: variant calling by GATK question about alignment
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rob.costa1234 • 190 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
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modified 2.2 years ago
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ijaz786besanttech • 0
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2.2 years ago by
rob.costa1234 • 190
Hello,
please provide us the complete error message and the output of
samtools view -H yourbamfile.bam
.fin swimmer