I work with HAPCUT software to make Haplotypes using a sorted bam file and a vcf file containing varients. 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
thanks for any advice on this problem.