Commit 2ed3631b authored by Robin Erich Muench's avatar Robin Erich Muench
Browse files

snpCaller options: SNP definitions

parent 1794b1b2
......@@ -65,7 +65,12 @@ static int print_usage()
fprintf(stderr, " -f, faidx indexed reference metagenome \n ");
fprintf(stderr, " -g, gene annotation file [NULL].\n");
fprintf(stderr, " -i, individual SNPs output file [NULL].\n\n");
fprintf(stderr, "SNP definition: \n");
fprintf(stderr, " -c, minimum coverage (mapped reads) per position [4]\n ");
fprintf(stderr, " -p, minimum non-reference nucleotide allele frequency per position [0.01].\n");
fprintf(stderr, " -t, minimum number of non-reference nucleotides per position [4].\n\n");
// fprintf(stderr, " -d,-a, for debugging only \n\n");
fprintf(stderr, "\n");
fprintf(stderr, "Note: Expecting samtools mpileup as standard input\n\n");
return 1;
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