Comments (1)
Hi,
We are planning to release a new version of elPrep soon that includes variant calling. We were not planning to add .bai index files. However, we are always willing to add new features, but we prioritize based on our funding resources.
Thanks.
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Related Issues (20)
- [RFE] haplotypecaller: support for custom GVCF GQ slices HOT 1
- Comment: handling RG's in SFM HOT 4
- GATK equivalency - version HOT 1
- Issue during build of v5.1.0 HOT 3
- Variant calling using `sfm` does not adhere to thread limit HOT 13
- "exit status 2" error HOT 2
- vcf-to-elsites HOT 3
- Proper running using sam input file? HOT 1
- coverage vs vcf.gz size discrepancy HOT 4
- elprep5: gVCF does not match BAM read pileup HOT 2
- `elprep split` output directory HOT 5
- Add wiki page about "creating your own `sfm` script" HOT 3
- header tag differs between runs HOT 2
- elprep merge: add input for intermediate files
- feature: index output HOT 2
- Very low number of variants called by elprep in an heterozygous genome
- elfasta-conversion error: bufio.Scanner: token too long HOT 6
- Option to output realigned BAM file during --haplotypecaller step
- build fails on ALMA linux 9
- NO_COOR error when trying to index the output bam file
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