User:Lindenb/Notebook/UMR915/20100628
From OpenWetWare
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
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
#sift accepts only file < 1Mb
split -C 900kB jeter.txt sift_
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;
