bcftools concat for denovo_rna_seq , concat make mistakes
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start at the bcftools concat entry point and inspect how the VCF header is checked against sequence names. Reproduce the reported error with the fasta_49.origin file, considering the samtools mpileup/call and bowtie2 transcript-level workflow. Done means determining whether the input is suitable and documenting or correcting the handling of the missing header sequence.
Written by the indexing model from the issue text.
Description
The sequence "TRINITY_DN76000_c7_g1" not defined in the header: /mnt/ilustre/users//snp_indel/fasta_49.origin
fasta_49.origin is a vcf file produced by samtools mpileup (bam file comes form bowtie2 in transcript level) and bcftools call , then make a transcript to unigene transversion, is this suitable, thanks a lot
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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