updated README, restored clinvar_alleles_example_750_rows.*.tsv sampl…

…e output files

.gitignore

@@ -15,6 +15,7 @@ src/last.dump.rda
 
 ### Heavy Data Files ###
 src/pipeline_output
+src/output_tmp
 src/logs
 *.old.*
 ClinVarFullRelease*

README.md

@@ -16,6 +16,8 @@ Each of these directories contains the following files:
 * __clinvar_alleles.*.tsv.gz__: table where each row represents a single variant allele. This is generated by grouping _clinvar_allele_trait_pairs.tsv.gz_ by allele.
 * __clinvar_alleles.*.vcf.gz__: _clinvar_alleles.tsv.gz_ converted to VCF format.
 * __clinvar_alleles_with_exac_v1.*.tsv.gz__: _clinvar_alleles.tsv.*.gz_ with additonal columns from the [ExAC v1](http://exac.broadinstitute.org/about) dataset that have non-empty values for all clinvar alleles that are also present in ExAC.  
+* __clinvar_alleles_with_gnomad_exomes.*.tsv.gz__: _clinvar_alleles.tsv.*.gz_ with additonal columns from the [gnomAD](http://gnomad.broadinstitute.org/about) dataset that have non-empty values for all clinvar alleles that are also present in the gnomAD exomes callset.  
+* __clinvar_alleles_with_gnomad_genomes.*.tsv.gz__: _clinvar_alleles.tsv.*.gz_ with additonal columns from the [gnomAD](http://gnomad.broadinstitute.org/about) dataset that have non-empty values for all clinvar alleles that are also present in the gnomAD genomes callset.  
 * __clinvar_alleles_stats.*.txt__:  summary of the different columns in _clinvar_alleles.*.tsv.gz_, along with some basic stats on the different values that appear in each column.
 
 
@@ -66,7 +68,7 @@ To run the pipeline:
 ```
 cd ./src
 pip install --user --upgrade -r requirements.txt
-python2.7 master.py --b37-genome /path/to/b37.fasta --b38-genome /path/to/b38.fasta -E /path/to/ExAC.r1.sites.vep.vcf.gz  
+python2.7 master.py --b37-genome /path/to/b37.fa --b38-genome /path/to/b38.fa -E /path/to/ExAC.r1.sites.vep.vcf.gz -GG /path/to/gnomad.genomes.r2.0.1.sites.coding.autosomes_and_X.vcf.gz -GE /path/to/gnomad.exomes.r2.0.1.sites.vcf.gz
 ```
 
 See `python master.py -h` for additional options.  

src/master.py

@@ -189,6 +189,7 @@ def download_if_changed(job_runner, local_path, ftp_host, ftp_path):
 
         # create uncompressed example files that contain the 1st 750 lines of the compressed tsvs so people can easily see typical values online on github
         job.add("gunzip -c IN:%(tmp_dir)s/clinvar_allele_trait_pairs.%(fsuffix)s.tsv.gz | head -n 750 > OUT:%(output_dir)s/clinvar_allele_trait_pairs_example_750_rows.%(fsuffix)s.tsv" % locals())
+        job.add("gunzip -c IN:%(tmp_dir)s/clinvar_alleles.%(fsuffix)s.tsv.gz | head -n 750 > OUT:%(output_dir)s/clinvar_alleles_example_750_rows.%(fsuffix)s.tsv" % locals())
         job.add("gunzip -c IN:%(tmp_dir)s/clinvar_alleles.%(fsuffix)s.vcf.gz | head -n 750 > OUT:%(output_dir)s/clinvar_alleles_example_750_rows.%(fsuffix)s.vcf" % locals())
 
         # create tsv table with extra fields from ExAC: filter, ac_adj, an_adj, popmax_ac, popmax_an, popmax