Ted Chiang

The genotypes for the HGDP (n=780) is public, and according to their blog, but some work would be needed to parse them into vcf formats for somalier to ingest. I...

Hi Josianne, I'm sorry about the issues. The basic idea is that it copies files from a directory containing GATK DoC files (ie. *.DATA.sample_interval_summary) to a midpool folder, ie.'testmidpool' as...

The GATK DoC file should have exactly the same coordinates as the panel file. ie. the first column of the *.DATA.sample_interval_summary Target 1:10356935-10357156 1:10357212-10357325 ... should be the same as...

Thank you for your interest in Atlas-CNV. 100 bp is not the average read length but the **actual** read length of the sequencing. We used paired-end reads from Illumina HiSeq...

Hi Xuan, Thank you for your interest in using Atlas-CNV. When you see a failed sample_id, it means it has failed the sampleQC=0.2 criteria (> 0.2). This was the valued...

(1) we use version 3 of the GATK software from Broad Institute to compute the Depth of Coverage on a given bam file.

Sorry for the late response. Hope the comments below helps. 1. For GATK, see the config file. In there is variable to specify the directory (and file name format) where...

Hi Oskar, Thank you for your interest in Atlas-CNV. Although, I haven't tested I think the R code should still work with newer versions of R as long as the...

Hi Oskar, Ah yes, it looks like some of the newer versions of those R packages are problematic. If you manage to get it to work in 3.1.1., then that...

Hi Oskar, I'm sorry for being slow to respond. Could you post a few lines of your input files? [--config config --panel Panel_final.txt --sample Samples_MiSeq_2.txt], so I can help debug?...