Comments (3)
Hi, If you're wanting to make mutations in a long-read genome (ONT) you could try addindel.py
with the options --aligner minimap --alignopts x:map-ont --single --force
and see how you go. Define the deletion you want to make as you would for an indel rather than as an SV e.g. chr5 70936274 70945251 1.0 DEL
.
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Thank you. Will try this.
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Hello,
When I try with the option minimap, I get the following error -
ValueError: ERROR unsupported aligner: minimap
I use v1.3. Please let me know if I should pull for the latest code.
Thanks,
Saranya
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Related Issues (20)
- Expansion repeats
- 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
- Losing Haplotype information 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
- 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
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