diff --git a/README.md b/README.md index ab6cf19dc37fcda0934b6b9a49c5a566e10d5d99..37df5837d90c5127c50834c832616d9b82e556c8 100644 --- a/README.md +++ b/README.md @@ -18,9 +18,11 @@ for deriving the inferred haplotype sequence against the list of SNP markers. ## Usage Obtain allele counts for cell barcodes listed in barcodeFile at the SNP positions in VCF from the BAM file. +``` Usage: sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix> + Options: -t --threads <threads> number of BAM decompression threads [default: 4] -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20] @@ -36,4 +38,4 @@ Options: Examples ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp- - +```