gcc -o vcftoFABIA vcftoFABIA.c -O3 gcc -o split_sparse_matrix split_sparse_matrix.c -O3 gunzip ALL.chr1.phase1_release_v2.20101123.snps_indels_svs.vcf.gz ./vcftoFABIA ALL.chr1.phase1_release_v2.20101123.snps_indels_svs ./ ## pars: 1) filename without .vcf 2) path ## NO .vcf !!!! ./split_sparse_matrix ALL.chr1.phase1_release_v2.20101123.snps_indels_svs _mat.txt 10000 5000 1 ## pars: 1) filename 2) extension 3) segment length 4) shift 5) annotation present