zstephens
commented
8 years ago If -M 0 and no input variants are present, then it would be expected that you get an empty VCF. In the second example where an input VCF is specified the output golden VCF should contain all the valid mutations that NEAT was able to insert into the data, so the fact that it is empty in this scenario is cause for concern.
Could you share the console output for the simulations? It would be useful to see if variants were being skipped, and for what reason. Alternatively, if you share a few lines from exac.vcf, I might be able to find some formatting/syntax that NEAT isn’t happy with.
-Zach
On Oct 13, 2016, at 12:30 PM, Stephen J Bush notifications@github.com<mailto:notifications@github.com> wrote:
The below commands create empty VCFs. The tumor run only had a vcf given for the last 6 runs.
I imagine this is because the normal run (a) had no VCF given and (b) no mutation rate (-M 0), while the tumor run (c) also had no mutation rate and (d) only included mutations present in the given VCF. It makes sense in this scenario that there is no need to create a VCF--is this correct / the expected behavior?
python /neat-genreads/genReads.py \ -R 126 -c 100 -M 0 --pe 300 30 \ -o /data/neat/vaf_15/normal \ -r /refs/ensembl/ensembl_build_75.fa \ -t /data/regions.bed \ --bam --vcf --job N 36
python /neat-genreads/genReads.py \ -R 126 --pe 300 30 -c 100 -M 0 \ -o /data/neat/vaf_15/tumor11 \ -t /data/regions.bed \ -r /refs/ensembl/ensembl_build_75.fa \ -v /refs/exac/exac.vcf \ --bam --vcf --job 1 36
Here's the directory output:
-rw-r--r-- 1 root root 821 Oct 13 12:24 tumor_golden.vcf.job01of36 -rw-r--r-- 1 root root 0 Oct 13 09:36 tumor_golden.vcf.job02of36 -rw-r--r-- 1 root root 0 Oct 13 09:30 tumor_golden.vcf.job03of36 -rw-r--r-- 1 root root 0 Oct 13 09:32 tumor_golden.vcf.job04of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job05of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job06of36 -rw-r--r-- 1 root root 0 Oct 13 09:32 tumor_golden.vcf.job07of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job08of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job09of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job10of36 -rw-r--r-- 1 root root 0 Oct 13 09:34 tumor_golden.vcf.job11of36 -rw-r--r-- 1 root root 0 Oct 13 09:34 tumor_golden.vcf.job12of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job13of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job14of36 -rw-r--r-- 1 root root 0 Oct 13 09:33 tumor_golden.vcf.job15of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job16of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job17of36 -rw-r--r-- 1 root root 0 Oct 13 09:33 tumor_golden.vcf.job18of36 -rw-r--r-- 1 root root 0 Oct 13 09:30 tumor_golden.vcf.job19of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job20of36 -rw-r--r-- 1 root root 0 Oct 13 09:36 tumor_golden.vcf.job21of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job22of36 -rw-r--r-- 1 root root 0 Oct 13 09:30 tumor_golden.vcf.job23of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job24of36 -rw-r--r-- 1 root root 0 Oct 13 09:34 tumor_golden.vcf.job25of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job26of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job27of36 -rw-r--r-- 1 root root 0 Oct 13 09:35 tumor_golden.vcf.job28of36 -rw-r--r-- 1 root root 0 Oct 13 09:29 tumor_golden.vcf.job29of36 -rw-r--r-- 1 root root 22125196019 Oct 13 15:06 tumor_merged_golden.bam -rw-r--r-- 1 root root 3284 Oct 13 15:06 tumor_merged_golden.vcf
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muppetjones
noellevb
The below commands create empty VCFs. The tumor run only had a vcf given for the last 6 runs.
I imagine this is because the normal run (a) had no VCF given and (b) no mutation rate (
-M 0), while the tumor run (c) also had no mutation rate and (d) only included mutations present in the given VCF. It makes sense in this scenario that there is no need to create a VCF--is this correct / the expected behavior?Here's the directory output: