TCGA Mutect2 and Strelka2 file appear to be identical?

[cansavvy]

What data file(s) does this issue pertain to?

pbta-tcga-snv-mutect2.vep.maf.gz and pbta-tcga-snv-strelka2.vep.maf.gz

What release are you using?

release-v13-20200116

Put your question or report your issue here.

Both have exactly 38296 number of mutation calls (number of rows) and the following prints out TRUE:

strelka_df <- data.table::fread("data/pbta-tcga-snv-strelka2.vep.maf.gz", data.table = FALSE)
mutect_df <- data.table::fread("data/pbta-tcga-snv-mutect2.vep.maf.gz", data.table = FALSE)

# This returns TRUE
all.equal(strelka_df, mutect_df)

# This returns TRUE as well
dplyr::all_equal(strelka_df, mutect_df)

Is there something I'm missing? Or did these file accidentally get mixed up?

[cansavvy]

I deleted the files and their redirects and re-ran bash download-data.sh and retried the above and am still getting TRUE? But the md5sum.txt file does show they are different.

93a91212e90b8c2533e8dfef9e72f7c2  pbta-tcga-snv-mutect2.vep.maf.gz
3c1f3fce62e4224fbb5466bd65516171  pbta-tcga-snv-strelka2.vep.maf.gz

[jharenza]

@yuankunzhu @tkoganti @migbro - can you look into this?

[cansavvy]

In Terminal, diff pbta-tcga-snv-mutect2.vep.maf.gz pbta-tcga-snv-strelka2.vep.maf.gz doesn't spit back anything, but as a positive control, I tried diff pbta-tcga-snv-lancet.vep.maf.gz pbta-tcga-snv-strelka2.vep.maf.gz and it showed me all the lines that were different.

[yuankunzhu]

@cansavvy i think we might have merged the same content for those two files. @tkoganti is checking and re-do it now. But a quick ls looks like those two files has a 1-byte file size off?

2020-01-16 18:31:25    8805609 data/release-v13-20200116/pbta-tcga-snv-mutect2.vep.maf.gz
2020-01-16 18:31:26    8805610 data/release-v13-20200116/pbta-tcga-snv-strelka2.vep.maf.gz

that would explain the md5 difference, but with exactly same mutation content. sorry for the confusion, we will fix this in a new release.

[tkoganti]

Hi @cansavvy I used strelka files for mutect by mistake. Sorry about that. I uploaded new strelka and mutect2 under V14 folder here -
https://cavatica.sbgenomics.com/u/cavatica/pbta/files/#q?path=processed-data-merge%2FV14-data&search=pbta-tcga

mutect2 file is 3.3Mb and strelka is 8.4Mb (file size for new maf.gz files )

[cansavvy]

@tkoganti , this seems to be telling me I don't have access to the link you posted?

[cansavvy]

Also, the files before were 8.8Mb, but now neither file is that size?

[tkoganti]

Both the new and old files have a file size of 8.4 Mb (8,805,610 bytes, it was showing as 8.4M when I looked at the files using ls -lh)

I did not realize you did not have access to cavatica. These files are in a staging area currently and we will let you know when they are released.

[jharenza]

@cansavvy if you have a CAVATICA username, we can add you to the project so you can preview the files. @tkoganti I am seeing that the Mutect2 gzipped maf is 3.3 MB and the Strelka2 gzipped maf is 8.4 MB - is this correct, or should Mutect2 be larger, as alluded to above?

[tkoganti]

@jharenza - See below for file sizes -

new and old strelka gzipped maf files - ~8.4M
old mutect file - ~8.4M (This was an error)
New mutect file - ~3.3M

[jharenza]

closed via #507