variant calling by GATK question about alignment

Question

[rob.costa1234]

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

[finswimmer]

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