Paweł Sztromwasser

exomiser does not output gnomAD and 1KG frequency annotations

9

Hi, After downloading exomiser 10.0.1 and 1802_hg19 dataset, I ran the NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38 example. Everything went fine, except that in the output several variant frequency annotations were missing. Here is the...

is it a good time for a reference genome switch?

5

Thank you for making this amazing set of resources available. It is not really an issue but a question about a strategic decision. If one was to start a project...

locating pairs in CRAM stopped working in versions after 1.0.1

1

Having BAM and CRAM created from it (`samtools view -CT $REFERENCE_FASTA bam > cram` I found that although version 1.0.1 works fine both files, more recent versions: - 1.0.2-rc1 -...

--force option

7

Hi, We noted that when the pipeline breaks, intermediate files are left in the output folder. To restart the analysis the output dir needs to be deleted. Have you considered...

resource consumption increase since 2.0.1

4

First of all thank you for the great work with the cgpwgs pipeline. We have been using version 2.0.1 and consider moving to 2.1.0 now, mainly due to the ASCAT/Caveman...