Comments (1)
Hi Bosh,
You are correct that the GENOME.WIDE.READ.COUNT is the total number of genome-wide filtered mapped reads, not simply the number of reads in the linked regions being tested. This is intentional, and the value is used as a scaling coefficient for each individual's read counts.
The way we do the shuffling is to shuffle the genotypes across individuals while preserving the counts. This way the region read counts are kept appropriately paired with the total read counts. The combined_test.py script has a --shuffle option that will do this for you.
Graham
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Related Issues (20)
- Missing step in CHT readme?
- Many reads discarded due to remapping with different CIGAR HOT 6
- CHT Snakemake workflow getting stuck at adjust_read_counts
- VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated
- find_intersecting_snps.py outputting sam files rather than bam files HOT 2
- Small sample size HOT 3
- filter_remapped_reads.py HOT 2
- find_intersecting_snps.py HOT 3
- Minor typo in Snakefile
- Represent phased blocks in VCF file HOT 1
- find_intersecting_snps.py: for pair in product(new_reads[0][group], new_reads[1][group]): IndexError: list index out of range HOT 1
- Whole genome sequencing data HOT 1
- running filter_remapped_reads.py on multiple samples all get empty bam files
- Incomplete h5 files with snp2h5
- filter_remapped_reads.py with bams created by HISAT2/ other mappers than Bowtie2 HOT 2
- running snp2h5 in the mapping snakemake HOT 1
- error in rule "get_as_counts" / bam2h5.py
- VCF to HDF5 Error
- Will rmdup_pe.py behave normally if one mate from a read pair is removed? HOT 1
- about NAs and 0s in CHT step 6 "extract_haplotype_read_counts"
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