Comments (3)
grep -P changed grep -E
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Hello,
Was the problem solved changing grep -P to grep -E?
from automap.
Hello, I also encountered this issue and figured it was because my input was a bgzipped file (.gz). After providing an unzipped VCF, I was able to run AutoMap without any issues. Putting this here for future users in case anyone else is facing this error.
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Related Issues (20)
- output.tsv not well sorted HOT 1
- Can it be used on RNA-seq data? HOT 1
- PASS filtering HOT 1
- Small misprint in AutoMap v1.2.0 TSV output footer HOT 1
- can it be used on non-human data? HOT 3
- How to calculate the fraction of the exome in ROH HOT 2
- AutoMap_v1.2.sh: line 326: [: : integer expression expected HOT 2
- common for a family HOT 7
- --vcflist option not available in v1.2 HOT 1
- Can we get the list of variants in the result? HOT 1
- Why some of the ROH are not detected? HOT 3
- Unable to find locale file in common_analysis.sh HOT 1
- Help in running automap
- Error HOT 1
- Empty output for the test case HOT 1
- getting bcftools error when running AutoMap_v1.2.sh script on singularity container HOT 2
- issues with bcftools version. HOT 1
- change v1.2 to v1.3 HOT 1
- How small the minimum ROH size threshold can be without losing reliability? HOT 1
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