bam2h5.py is a python program for converting BAM files to read count HDF5 files. Specifically, bam2h5.py counts the number of reads that match the alternate and reference allele at every SNP in the provided SNP HDF5 data files. The read counts are stored in specified HDF5 output files.
Additionally counts of all reads are stored in another track (at the left-most chromosome position of the reads).
This program does not perform filtering of reads based on mappability. It is assumed that the inpute BAM files are filtered appropriately prior to calling this script.
Reads that overlap known indels are not included in allele-specific counts.
bam2h5 requires the pysam python library
bam2h5.py OPTIONS BAM_FILE1 [BAM_FILE2 ...]
Aligned reads are read from one or more BAM files. The provided BAM files must be sorted and indexed.
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--chrom CHROM_TXT_FILE [required]
Path to chromInfo.txt file (may be gzipped) with list of chromosomes for the relevant genome assembly. Each line in file should contain tab-separated chromosome name and chromosome length (in basepairs). chromInfo.txt files can be downloaded from the UCSC genome browser. For example, a chromInfo.txt.gz file for hg19 can be downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/
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--snp_index SNP_INDEX_H5_FILE [required]
Path to HDF5 file containing SNP index. The SNP index is used to convert the genomic position of a SNP to its corresponding row in the haplotype and snp_tab HDF5 files.
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--snp_tab SNP_TABLE_H5_FILE [required]
Path to HDF5 file to read SNP information from. Each row of SNP table contains SNP name (rs_id), position, allele1, allele2.
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--haplotype HAPLOTYPE_H5_FILE [optional]
Path to HDF5 file to read phased haplotypes from. If supplied, when read overlaps multiple SNPs counts are randomly assigned to ONE of the overlapping HETEROZYGOUS SNPs; if not supplied counts are randomly assigned to ONE of overlapping SNPs (regardless of their genotype).
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--samples SAMPLES_TXT_FILE [optional]
Path to text file containing a list of individual identifiers. The ordering of individuals must be consistent with the haplotype file. The samples file is assumed to have one identifier per line in the first column (other columns are ignored).
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--individual INDIVIDUAL [optional]
Identifier for individual, used to determine which SNPs are heterozygous. Must be provided if --haplotype argument is provided and must match one of the individuals in the file provided with --samples argument.
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--data_type uint8|uint16
Data type of stored counts; uint8 takes up less disk space but has a maximum value of 255 (default=uint8).
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--ref_as_counts REF_AS_COUNT_H5_FILE [required]
Path to HDF5 file to write counts of reads that match reference allele. Allele-specific counts are stored at the position of the SNP.
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--alt_as_counts ALT_AS_COUNT_H5_FILE [required]
Path to HDF5 file to write counts of reads that match alternate allele. Allele-specific counts are stored at the position of the SNP.
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--other_as_counts OTHER_AS_COUNT_H5_FILE [required]
Path to HDF5 file to write counts of reads that match neither reference nor alternate allele. Allele-specific counts are stored at the position of the SNP.
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--read_counts READ_COUNT_H5_FILE [required]
Path to HDF5 file to write counts of all reads, regardless of whether they overlap a SNP. Read counts are stored at the left-most position of the mapped read.
# write HDF5 read count files for individual 18505
INDIVIDUAL=18505
./bam2h5/bam2h5.py --chrom chromInfo.hg19.txt \
--snp_index snp_index.h5 \
--snp_tab snp_tab.h5 \
--haplotype haps.h5 \
--samples H3K27ac/samples.txt \
--individual $INDIVIDUAL \
--ref_as_counts ref_as_counts.$INDIVIDUAL.h5 \
--alt_as_counts alt_as_counts.$INDIVIDUAL.h5 \
--other_as_counts other_as_counts.$INDIVIDUAL.h5 \
--read_counts read_counts.$INDIVIDUAL.h5 \
H3K27ac/$INDIVIDUAL.chr*.keep.rmdup.bam