User:Lindenb/Notebook/UMR915/20100716

20100714        Top        20100722       

• show interface to RR
• starting creating a linkage with BDB
• normalized the database with UMR915DBNormalisation
• downloaded the data for the new project (see mail Jul 16 2010 09H52 )
• added critical distance between variations.

loading GATK variations

loading GATK variations with UnifiedGenotyper. Something like:

 ~/bin/insertvariants.sh -C -s X1 -d "bwa/recal GATK UnifiedGenotyper X1 20100709" -t vcf -cfg  ~/.umr915.properties gatk_call_X1.vcf.gz

generating new input for sift

 split -C 900k  jeter.sift.input.txt  sift_

and for polyphen

removing duplicate in the database

after normalisation, remove duplicates in sift and polyphen:

  mysql -N -u anonymous -e 'select id from sift group by variation_id,alt having count(*)!=1' umr915 |\
    awk '{printf("delete from sift where id=%s;\n",$1);}'
  mysql -N -u anonymous -e 'select id from polyphen group by variation_id,alt,library having count(*)!=1' umr915 |\
    awk '{printf("delete from polyphen where id=%s;\n",$1);}' > jeter.sql

compare SIFT/polyphen

 select P.prediction as "polyphen",S.prediction as "sift",count(*) from polyphen as P, sift as S where P.variation_id=S.variation_id and P.alt=S.alt and P.library="HumVar" group by 1,2 order by 1,2

Polyphen HumVar

polyphen	sift	count(*)
PROBABLY_DAMAGING	NULL	5
PROBABLY_DAMAGING	UNSCORED	437
PROBABLY_DAMAGING	TOLERATED	3156
PROBABLY_DAMAGING	DAMAGING_LOW	3616
PROBABLY_DAMAGING	DAMAGING	5773
POSSIBLY_DAMAGING	NULL	23
POSSIBLY_DAMAGING	UNSCORED	576
POSSIBLY_DAMAGING	TOLERATED	6934
POSSIBLY_DAMAGING	DAMAGING_LOW	4549
POSSIBLY_DAMAGING	DAMAGING	3053
BENIGN	NULL	40
BENIGN	UNSCORED	1009
BENIGN	TOLERATED	20032
BENIGN	DAMAGING_LOW	5135
BENIGN	DAMAGING	1692
UNKNOWN	NULL	6
UNKNOWN	UNSCORED	636
UNKNOWN	TOLERATED	3037
UNKNOWN	DAMAGING_LOW	2838
UNKNOWN	DAMAGING	255

Polyphen HumDiv

polyphen	sift	count(*)
PROBABLY_DAMAGING	NULL	12
PROBABLY_DAMAGING	UNSCORED	681
PROBABLY_DAMAGING	TOLERATED	5545
PROBABLY_DAMAGING	DAMAGING_LOW	5597
PROBABLY_DAMAGING	DAMAGING	6951
POSSIBLY_DAMAGING	NULL	15
POSSIBLY_DAMAGING	UNSCORED	407
POSSIBLY_DAMAGING	TOLERATED	5413
POSSIBLY_DAMAGING	DAMAGING_LOW	3283
POSSIBLY_DAMAGING	DAMAGING	1854
BENIGN	NULL	41
BENIGN	UNSCORED	934
BENIGN	TOLERATED	19164
BENIGN	DAMAGING_LOW	4420
BENIGN	DAMAGING	1713
UNKNOWN	NULL	6
UNKNOWN	UNSCORED	636
UNKNOWN	TOLERATED	3037
UNKNOWN	DAMAGING_LOW	2838
UNKNOWN	DAMAGING	255