teepean
teepean
I ran into the same problem. bcftools +liftover -vv -Ou snps_hg38.vcf.gz -- -s GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -f human_g1k_v37.fasta -c GRCh38_to_GRCh37.chain.gz --reject reject.vcf --reject-type u --write-src | bcftools sort -o output.vcf -Oz plugin...
bcftools +liftover -V bcftools 1.21 using htslib 1.21 plugin at 1.21 using htslib 1.21 The original VCF is here: https://ybrowse.org/gbrowse2/gff/snps_hg38.vcf.gz
Thanks! Honestly if this is not me and the LLM hallucinating together, this would be one step forward replacing bwa aln as de facto ancient DNA aligner.
These are the commands used to determine and compare the quality of the reads. samtools flagstat: Basic mapping statistics (total reads, mapped reads, percentages) samtools stats: Comprehensive quality metrics (error...
I was reading Joshua Rubin's preprint SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings and it mentioned SHRiMP "SHRiMP is quite a sensitive alignment tool for aDNA samples but...
The root cause was that the file was created from a GRCh38 CRAM with WGSExtract and the 23andme header still has mentions of build 37.
I think WGSExtract needs to be fixed to create a compatible header depending on the build.
To be honest that would be the best solution.