README
¶
bio-pileup
Given a BAM or PAM, and a BED file describing genomic positions of interest, bio-pileup reports the number of reads supporting each allele at each position. This command is similar to "bcftools mpileup".
There are options for "collapsing" the two ends of a read-pair together, or entire duplicate-sets ("bags") identified by doppelmark.
Only SNPs are currently reported, but indel support is very likely to be added in the future.
Sample usage:
bio-pileup
--bed my-regions.bed
--out output-prefix
my.bam
ref.fa
Run "bio-pileup --help" for more details.
Documentation
¶
Overview ¶
Given a BAM or PAM, and a BED file describing genomic positions of interest, bio-pileup reports the number of reads supporting each allele at each position. This command is similar to "bcftools mpileup".
There are options for "collapsing" the two ends of a read-pair together, or entire duplicate-sets ("bags") identified by doppelmark.
Only SNPs are currently reported, but indel support is very likely to be added in the future.
Sample usage:
bio-pileup \
--bed my-regions.bed \
--out output-prefix \
my.bam \
ref.fa
Copyright 2020 Grail Inc.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Source Files