Where are the WXS samples in the Lancet dataset?

[cansavvy]

File(s)

The Lancet MAF file: pbta-snv-lancet.vep.maf.gz doesn't appear to have WXS samples. Is this how it is supposed to be?

Release

v5 release-v5-20190924

Link to OpenPBTA-manuscript

In the methods section don't see an indication in the methods that Lancet wasn't run on the WXS files, unless I'm missing that.

https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md#somatic-single-nucleotide-variant-calling

Question/issue

It looks like there are no WXS samples in the Lancet dataset? Should that be the case?

# Read in this MAF, skip the version number
maf_df <- data.table::fread("data/pbta-snv-lancet.vep.maf.gz", skip = 1, data.table = FALSE)

# Isolate metadata to only the samples that are in the datasets
metadata <- readr::read_tsv("data/pbta-histologies.tsv") %>%
  dplyr::filter(Kids_First_Biospecimen_ID %in% maf_df$Tumor_Sample_Barcode) %>%
  dplyr::distinct(Kids_First_Biospecimen_ID, .keep_all = TRUE) %>%
  dplyr::arrange() %>%
  dplyr::rename(Tumor_Sample_Barcode = Kids_First_Biospecimen_ID) %>%
  readr::write_tsv(metadata_file)

summary(as.factor(metadata$experimental_strategy))

Output from above is WGS 940.

[jharenza]

@cansav09 should not be the case. @bmennis - see this issue as well - looks like the WXS files were missed here.

[jharenza]

Update: it looks like WXS samples were not run, so they are being added to the queue ASAP. Related to #135 (also need to be run for Vardict).

[jharenza]

As an update, we have completed this and they will be ready for #146