Changeset 5811


Ignore:
Timestamp:
Jan 16, 2020, 8:33:18 AM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1222: Remove the G5 distance calculations from the variant calling script

Removed code for doing G5 distance calculcations and annotations

File:
1 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

    r5809 r5811  
    348348      script.cmd("cp ${ScriptDir}/stderrwrap.sh .");
    349349      script.cmd("cp ${ScriptDir}/gc_stat.py .");
    350       script.cmd("cp ${ScriptDir}/g5_dist.py .");
    351350      script.cmd("cp ${ScriptDir}/gc_stat.toml .");
    352       script.cmd("cp ${ScriptDir}/g5_dist.toml .");
    353351      script.cmd("cp ${ScriptDir}/mutation_signature.R .");
    354352      script.cmd("cp ${ScriptDir}/Rscript.sh .");
     
    432430      {
    433431        script.cmd("if [ $NUMVARIANTS -gt 0 ]; then");
    434         script.comment("Calculate distance to closest G5 SNP and add back");
    435         script.comment("annotations DIST_SNP and DIST_DIV to the variants VCF");
    436         script.cmd("awk '{OFS=\"\\t\"; if (/^chr/){print $1,$2-1,$2,$4,$5}}' tmp/variants-raw-2.vcf | sort -k 1,1 -k2,2n > tmp/variants-raw.bed");
    437         script.cmd(bedtools_path+" closest -d -t first -a tmp/variants-raw.bed -b ${BaseDir}/dbsnp/dbsnp_g5_snv.bed.gz > tmp/g5-dist-1.bed");
    438         script.cmd(bedtools_path+" closest -d -t first -a tmp/g5-dist-1.bed -b ${BaseDir}/dbsnp/dbsnp_g5_div.bed.gz > tmp/g5-dist-2.bed");
    439         script.cmd("cat tmp/g5-dist-2.bed | ./g5_dist.py | bgzip -c > tmp/g5-dist.vcf.gz");
    440         script.cmd("tabix tmp/g5-dist.vcf.gz");
    441         script.cmd("./stderrwrap.sh " + vcfanno_path + " g5_dist.toml tmp/variants-raw-2.vcf > tmp/variants-annotated-1.vcf 3>> vcfanno.out");
    442         script.newLine();
    443        
    444432        String annoCmd = "./stderrwrap.sh " + vcfanno_path;
    445433        annoCmd += " " + vcfanno_options;
    446         annoCmd += " tmp/variants-annotated-1.vcf";
     434        annoCmd += " tmp/variants-raw-2.vcf";
    447435        annoCmd += " > tmp/variants-annotated-2.vcf";
    448436        annoCmd += " 3>> vcfanno.out";
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