Comments (3)
Could be that the -Q 5
option is filtering all mappings. You may want to verify your gam
has MAPQ values (vg view -a | grep
mapping_quality`). If this is the issue (they default to 0 if unspecified), you cna rerun without the filter, or try changing your GraphAligner options to output MAPQs.
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I vaguely recall that GraphAligner might not be able to output mapping qualities. It would be worth checking me on this though.
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It used to not output MAPQs but from what I understand newer versions should have them maickrau/GraphAligner#75 (comment)
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Related Issues (20)
- Program stuck at [IndexRegistry]: Chunking VCF(s) for days HOT 2
- vg alignments not reporting split reads HOT 1
- Mapping paired end reads with vg giraffe: "Falling back on single-end mapping" HOT 9
- Autoindex should parse tabix-indexed monolithic VCFs in parallel
- vg pack error HOT 3
- VCF file empty when calling SV on ONT data HOT 9
- vg map errors HOT 5
- Genotyping SVs in a minigraph-cactus graph yields many similar alleles in output vcf HOT 1
- How to align both long and paired end short reads using vg HOT 1
- Augmentation failed on one chromosome, but succesfull on other chromosomes HOT 3
- Can VG simulate the third-generations long reads? HOT 5
- Issue with vg map and vg augment for certain inputs. HOT 2
- Merging multiple graph files HOT 4
- short read giraffe alignment crashes most of the time, works on a few random samples - Signal 11 HOT 2
- Running VG deconstruct failed in the gfa generated from PGGB pipline HOT 3
- ERROR vg autoindex :Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes (line 4). ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex) HOT 1
- Error Exceeded Limit of Size on Disk While Running vg index HOT 1
- Mapping paired reads w/ giraffe, no EOF marker, job stalls, exit code 79 HOT 5
- Construct a generation-level pan-genome HOT 5
- Release vg v1.58.0
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