User:Lindenb/Notebook/UMR915/20100628

=how many variations in the previous pileup?= for F in recal_bwa_rmdup_Brs*gz; do echo -n "$F "; gunzip -c $F | wc -l ; done recal_bwa_rmdup_Brs10.pileup.gz 118113 recal_bwa_rmdup_Brs1.pileup.gz 92292 recal_bwa_rmdup_Brs2.pileup.gz 92586 recal_bwa_rmdup_Brs3.pileup.gz 94320 recal_bwa_rmdup_Brs4.pileup.gz 91001 recal_bwa_rmdup_Brs5.pileup.gz 97320 recal_bwa_rmdup_Brs6.pileup.gz 90225 recal_bwa_rmdup_Brs7.pileup.gz 97952 recal_bwa_rmdup_Brs8.pileup.gz 96436 recal_bwa_rmdup_Brs9.pileup.gz 103912 =insert variations in DB= ~/bin/insertvariants.sh -s XX -C -d "bwa recal rmdup for XX" -type pileup recal_bwa_rmdupXX.pileup.gz

hum.. some variation in pileup where alt=ref. Remove those var: mysql -u root -D umr915 -N -e 'select id from variation where ref=alt ' |\ awk '{printf("delete from vcf_call where varation_id=%s;\ndelete from variation where id=%s;\n",$1,$1);}' > jeter.sql =generating input for PPH2= mysql -u root -D umr915 -N -e 'select concat(chrom,":",position+1),concat(ref,"/",alt) from variation where ref in ("A","T","G","C") and alt in ("A","T","G","C")' > jeter.txt wc -l jeter.txt 271938 jeter.txt =wrote a tool for reading SIFT= http://code.google.com/p/code915/source/browse/trunk/tools/src/java/fr/inserm/umr915/tools/SiftToSQL.java =generating for SIFT= mysql -h 172.18.241.112 -u anonymous -D umr915 -N -e 'select chrom,position+1,1,concat(ref,"/",alt) from variation where ref in ("A","T","G","C") and alt in ("A","T","G","C")' |\ sed 's/^chr//' | tr "   " "," > jeter.txt split -C 900kB jeter.txt sift_
 * 1) sift accepts only file < 1Mb

=table for sift= mysql table for sift:

create table sift( id int unsigned primary key auto_increment,  variation_id  int unsigned not null,  index(variation_id),  foreign key(variation_id) references variation(id) on delete cascade,  meta text,  creation datetime,  modified timestamp,  prediction enum("DAMAGING" , "DAMAGING *Warning! Low confidence." , "Not scored", "TOLERATED"), score float ,  median_info float  )  engine=InnoDB;