With respect to the reference sequence hg38 and gatkbundlehg38, I used gatkbundlehg38 and hg38.fa for alignment of exome sequence. I am getting error while using samtools reheader.
my command is:
path/to/samtools reheader -i HG100.sam > HG100.bam
I got following error both the times.
[E::hts_open] fail to open file '-i' [main_reheader] fail to read the header from -i.
HG100.sam is 4.9GB
Following shows it's header details:
@SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529 @SQ SN:chr3 LN:198295559 @SQ SN:chr4 LN:190214555 @SQ SN:chr5 LN:181538259 @SQ SN:chr6 LN:170805979 @SQ SN:chr7 LN:159345973 @SQ SN:chr8 LN:145138636 @SQ SN:chr9 LN:138394717 @SQ SN:chr10 LN:133797422