Darek Kedra

Hello, An interesting take on VCF storage. I assume that the VCFShark files need to be converted to bcf / VCF format before being usable by bcftools, correct? DK

Hello, First things first: thank you so much for creating a very useful tool. Modest enhancement proposal: genomic fasta files are fairly big, so I tend to keep them compressed...

alingment ID in STOCKHOLMs output

2

Hello, I used mlocarna to align tRNA isoforms. All works fine as far as I can tell, but the STOCKHOLM format files do not contain identifiers (which is to be...

Hello, ``` git clone --recursive [email protected]:arq5x/lumpy-sv.git ``` gives an error, whereas: ``` git clone --recursive https://github.com/arq5x/lumpy-sv ``` works fine. Hope it helps, Darek Kedra

wrong numbers with some BAMs

3

I got bizarre looking numbers for coverage on just single BAM file (one line of the output): 1|F0008AAR.2 998 999 A 50 50 0 140735599270096 140435982010547 1 140435981676544 67669007 636900700782336...

Hello, when clicking at the link: OMIM HPO-Gene mapping http://compbio.charite.de/jenkins/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt I am getting: ``` HTTP ERROR 404 Problem accessing /jenkins/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt. Reason: Not Found ``` Hope it helps Darek Kedra

Hello, looks like the sicer2 did implement the fix to handle beyond the ends of chromosomes reads. But somehow the results between these two programs differ. epyc2: 13_642 peaks, sicer2...

parallel implementations and clustering of reads

1

Hello, there are mature, included in the major Linux distros programs such as pigz, pbizp2 and lbzip2. These compress faster while being on par on compression ratios. The last one...

Hello, would it be possible for the more IT than GWAS crowd to have a fool-proof table along the lines: ``` beta_col => ES pval_col => LP se_col => SE...

check for the chrom names in the input vs dbSNP & reference fasta

1

Hello, Would it be possible to add an extra check for chr name in the gwas/TSV input not present in the genomic fasta and/or dbSNP file? I am aware that...