I work with HAPCUT software to make Haplotypes using a sorted bam file and a vcf file containing variants. When I run this command,
./extract_hairs --VCF variantfile.VCF --bam alignedreads.sorted.bam --maxIS 600 > fragment_matrix_file
an error says that
[bam_header_read] EOF marker is absent
Also before that, when I tried to sort bam file with samtools this error occurred. but samtools continued to make sorted bam and then I used it in HAPCUT.
Thanks for any advice on this problem.