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jpuritz
a bash pipeline for RAD sequencing
This PR attempts to fix the issues described in #83 by leveraging `find`. - In cases where `ls` is used to search for wildcard-ed files, `find` is restricted to `-maxdepth...
I haven't experienced this directly, but was contacted by someone using dDocent on a lot of samples such that calls to `ls` piped into other things created errors where the...
I've noticed that missing data in my merged vcf file following genotyping are haploid ".:" while all genotypes with data are correctly diploid. Running the` sed -e 's/ \.\:/ \.\/\.\:/g'...
I recently had variant calling finish, and somewhere in the terminal log was a minor mention of mawk being unable to open `mapped.somenumber.bed` because of an open file limit. The...
Hey, I have been experimenting with some of my datasets and I have found that filtering the bam files prior to SNP calling not only reduces the number of SNPs...
Solution confirmed on 3 different HPC: ```bash # add the following line prior to parallel --env line, which saves the whole current environment parallel --record-env # modify by replacing --env...
### suggestion apply a minimum coverage filter to the `cov.stats` prior to making the `mapped.*.bed` files, which will ultimately reduce the number of contigs genotyped ### the minimum coverage value...
Is it intended that the numbers of heterozygotes with read depth equal to 4 and 5 are not being calculated in the script? If so, could you explain the reason?...
I was running denovo assembly on SE RAD-seq reads, and prepared all infile and config.ctl file according to dDocent manual. The program runs with an error somewhere in bwa saying:...
Received this error: Creating alignment intervals mawk: cannot open "mapped.2918.bed" for output (Too many open files) Genomic interval creation failed. This may be related to the maximum number of open...
