Comments (2)
Hi, do you mean haplotype tags i.e. HP/PS/PC are present before addindel and missing afterwards?
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hey,
yes exactly. But It is missing only for the reads on which the mutation was added.
from bamsurgeon.
Related Issues (20)
- addindel.py error: Could not pile up over region - no successful mutations HOT 3
- ValueError: invalid contig `22` addindel.py failed. HOT 2
- Unexpected deletions around Inversion and Translocation
- All avgoutcoverage = 0 HOT 4
- no succesful mutations with addsv.py
- Clarification on editing of MNVs HOT 2
- ValueError: quality and sequence mismatch: 98 != 97 HOT 5
- Dockerfile installation issue HOT 3
- AttributeError: 'array.array' object has no attribute 'tostring' HOT 5
- outbam HOT 7
- Publish docker image on Github Container Registry
- Add SV for Single end ONT reads HOT 3
- Release to pull in some new fixes HOT 4
- replace_reads.py only writing out one read of each pair for paired end. HOT 8
- Samtools view issue
- Bamsurgeon goes silent (does not finish) on high coverage small panel bam file HOT 8
- [Enhancement] Specify vcf output path in addsv.py
- "best contig too short to make mutation" / "No good alignment between mutated contig and original, aborting mutation!" Errors
- Bamsurgeon addsnv.py takes 4 hours to add one SNP to a bam file of size 3.1MB ?
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