count-reads-fw

NOTE: This function (formerly called comBBo) uses the legacy fixed-width binning described in the HATCHet paper. We recommend using count-reads and combine-counts which apply an adaptive binning scheme to ensure that each genomic bin has comparable BAF signal.

This step of HATCHet splits the human reference genome into fixed-width bins (i.e., small genomic regions), and computes the number of sequencing reads aligned to each bin from every given tumor samples and from the matched normal sample.

Input

count-reads-fw takes in input sorted and indexed BAM files for multiple tumor samples from the same patient, a sorted and index BAM file from a matched-normal sample, and a indexed human reference genome.

Name	Description	Usage
-T, --tumors	A white-space separated list of sorted-indexed BAM files for tumor samples	The tumor samples from the same patient that are jointly analyzed by HATCHet
-N, --normal	A sorted-indexed BAM file for matched-normal sample	The matched normal sample for the same patient
-r, --reference	A FASTA file	The human reference genome used for germline variant calling

Output

count-reads-fw produces three tab-separated files: the first contains the read counts for every genomic bin in every tumor sample (raw counts not normalized), the second contains the read counts for every genomic bin the matched-normal sample (raw counts not normalized), and the third contains a list of the genomic positions that have been identified as germline heterozygous SNPs in the matched-normal sample.

Name	Description
-O, --outputnormal	The output file for the read counts from matched-normal sample
-o, --outputtumors	The output file for the read counts from the tumor samples

Main parameters

count-reads-fw

Optional parameters