Comments (2)
gmcvicker
commented on July 29, 2024
Hi Anto,
My opinion is that filtering on MAPQ10 or MAPQ20 should be fine and should not result in the loss of an excessive number of reads.
One caveat is that the mapping quality of a read could potentially differ depending on what allele is present in a read. Therefore, to avoid bias I would recommend doing the MAPQ filtering as part of both the initial mapping (Step 1) and remapping (Step 3) steps of the pipeline.
Hope this helps,
Graham
from wasp.
commented on July 29, 2024
Hi Graham,
many thanks. I have done as you recommended, providing as additionally filtering for properly paired
reads.
Thanks,
antonino
from wasp.
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 1
- Small sample size HOT 3
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- Minor typo in Snakefile
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- 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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