martinghunt

Minimum read length needed for genotype_sv?

5

I've been running tests on various data sets, and have had a few cases where `graphtyper genotype_sv` makes VCFs with almost every site having zero depth and a genotypes of...

Add an option that will let the user pass arbitrary options to the assembler.

breaks `clockwork map_reads` because command line parsing gets messed up.

Import checks that the fwd/rev FASTQ files are valid FASTQ, and have the same number of reads. The read names can mismatch between the fwd/rev files, but still import. Then...

because somehow "Illumina HiSeq 4053" got through import

Need to: - find all import_status == -1 - remove corresponding rows from Sample,Isolate,Seqrep tables - delete dirs on disk

script is not using datset_name and returns all samples

eg if IDs found to be wrong for an entire dataset and need changing to something else.

Imputation and null genotypes/indels

10

We've encountered some unexpected behaviour at a position where many of the samples have a deletion, and so have null genotype calls in the VCF file. Could you please advise?...