3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Calling Your Own Genome, December 2014 (view source)
Revision as of 00:08, 9 December 2014
, 00:08, 9 December 2014→Indel Step 2 (Day 2): Checking Indel
This will resume an already running screen.
This will resume an already running screen.
=== Looking at INDEL results ===
Look in the output directory
ls ~/$SAMPLE/output
What in that directory was produced by indel calling?
* <code>gotcloud.indel.conf</code>
** dump of all configuration settings for this run
* <code>gotcloud.indel.Makefile</code>
** Makefile that was generated to manage all of the commands to be run
* <code>gotcloud.indel.Makefile.log</code>
** log of all commands run by the Makefile
* <code>indel/</code>
** indel output directory
Let's look at the indel output
ls ~/$SAMPLE/output/indel
* 3 directories
** aux - intermediate files
** indelvcf - intermediate files
** '''final indel files'''
Final indel directory:
ls ~/$SAMPLE/output/indel/final
* '''all.genotypes.vcf.gz - output VCF'''
* '''all.genotypes.vcf.gz.tbi - output VCF index file to allow jumping to positions'''
* all.genotypes.vcf.gz.tbi.OK - completion indicator
* merge/ - directory with per chromosome bcf (binary vcf) files
* all.genotypes.vcf.gz.OK - completion indicator
* all.genotypes.vcf.gz.tbi.log - log
* concat.log - log
</div>
</div>
</div>
</div>
==== Looking at final INDEL VCF ====
Check the number of passing INDEL variants:
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS"
Gives something like:
no. Indels : 570661
2 alleles (ins/del) : 570661 (0.87) [265448/305213]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
Check the number of passing INDEL's with allele count > 0:
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC!=0"
Gives something like:
no. Indels : 549963
2 alleles (ins/del) : 549963 (0.91) [261480/288483]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
Some INDELs had allele count 0.
Check the number of passing INDEL's with allele count 2:
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC==2"
Gives something like:
no. Indels : 216134
2 alleles (ins/del) : 216134 (1.17) [116511/99623]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
Check the number of passing INDEL's with allele balance > 0.5:
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AB>0.5"
Gives something like:
no. Indels : 132878
2 alleles (ins/del) : 132878 (0.68) [53714/79164]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
Check the number of passing INDEL's with allele balance < 0.5:
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AB<0.5"
Gives something like:
no. Indels : 169198
2 alleles (ins/del) : 169198 (0.89) [79504/89694]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
