User:Lindenb/Notebook/UMR915/20100621

loading tables from ucsc
wget "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz" wget "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.sql" wget "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp129.sql" wget "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp129.txt.gz" mysql -D hg18 < knownGene.sql mysql -D hg18 < snp129.sql mysql -D hg18 -e "load data local infile '/GENOTYPAGE/data/pubdb/ucsc/hg18/database/snp129.txt' into table snp129" mysql -D hg18 -e "load data local infile '/GENOTYPAGE/data/pubdb/ucsc/hg18/database/knownGene.txt' into table knownGene" create table baitlibrary_item(id int unsigned primary key auto_increment, baitlibrary_id int unsigned references baitlibrary(id), chrom enum("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrMT", "chrX", "chrY"), chromStart int unsigned not null, chromEnd int unsigned not null); alter table baitlibrary_item add index(chrom); alter table baitlibrary_item add index(chrom,chromStart);

Adding user
create user '....'@'....' grant select on umr915.* to '....'@'....'

compute overlap dindel/DBs for SLS2
script:

egrep -v '^#' XXXX1_variantCalls.VCF | sed 's/^/chr/' > /tmp/jeter.txt echo "create temporary table T1 	(  	chrom varchar(50) not null,  	pos int unsigned not null,  	id varchar(50),  	ref varchar(100),  	alt varchar(100),  	qual varchar(100),  	filter varchar(100),  	info varchar(100),  	format varchar(100),  	sample varchar(100),  	index (chrom),  	index (chrom,pos)  	);  load data local infile '/tmp/jeter.txt' into table T1;  delete from T1 where length(T1.alt)<=1;  delete from T1 where filter!='.';  select distinct  T1.*,  	S.name as 'SNP129_name',  	S.observed as 'SNP129_observed',  	S.class as 'SNP129_class',  	S.avHet as 'SNP129_avHet',  	K.name as 'KnownGene_name',  	K.proteinID as 'KnownGene_proteinID'  from  	(T1,  	umr915.baitlibrary_item as BI )  left join snp129 as S  	on S.chrom=T1.chrom and ((T1.pos-1)>=S.chromStart and (T1.pos-1) < S.chromEnd)  left join knownGene as K  	on K.chrom=T1.chrom and ((T1.pos-1)>=K.txStart and (T1.pos-1) < K.txEnd) where BI.chrom=T1.chrom and (T1.pos>=BI.chromStart and T1.pos <= BI.chromEnd) ; "

=Fonts for ubuntu= Fonts the the 48H00 of UMR915

as seen on http://ubuntuforums.org/showthread.php?t=85139

cd /usr/share/fonts/truetype sudo mkdir myfonts cd myfonts sudo cp ~/*.ttf. sudo chown root.root *.ttf sudo mkfontdir cd .. fc-cache

=why did I miss chr10:1036884 in my BAM ?== samtools view bwa_rmdup_XXXX1.bam chr10:1036884-1036884 |\ samtools view -S -b -T ${HG18} - > jeter2.bam samtools index jeter2.bam

ok, mutation in chr10:1036884:

samtools pileup -v -c -f ${HG18} jeter2.bam | samtools.pl varFilter -d 4  -D 1200  -Q 25 chr10	1036884	C	Y	11	11	56	96 ,$,$,$,$,$,...,,,,.,,,,...........t.......t..t...tt......,tttt.,tttt,.t,+1t.ttt..tttttttt.ttttt^]t^]t^]t^],^]t^]t^]t^]t^]t	IHCFIE?FEIGIIFBICICCDCFFF@DFG)FFGG@FF0CF)CFD7@FFEF=B.0&=7E375800F&8F+:0FF59938;;;B:7?8=,+-+)>5)+

ok, the line is still here

But when my program 'pileupfilter.jar -min-sq 25' is used, there is no more input. [http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output. SNP quality] is column[5](0)='11' < 25 → excluded ! So what was SLS2's quality for this SNP ?

when I used the recalibrated file: samtools view recal_bwa_rmdup_XXXX1.bam chr10:1036884-1036884 | samtools view -S -b  -T  ${HG18} - > jeter2.bam samtools index jeter2.bam samtools pileup -v -c -f ${HG18} jeter2.bam |samtools.pl varFilter -d 4 -D 1200  -Q 25 chr10	1036884	C	Y	21	21	56	96	,$,$,$,$,$,...,,,,.,,,,...........t.......t..t...tt......,tttt.,tttt,.t,+1t.ttt..tttttttt.ttttt^]t^]t^]t^],^]t^]t^]t^]t^]t	??=>?>;<=B@CC?;C>CDDEEDDDCDDD(DDDDBDD/DD)DCC7@CCCC>B,0&?9C446:23C&9C-=3BB7;76;:<>A=:A;@.,0.+63*,

the recalibrated file change the SNP quality, but is is still not high enough to be displayed for snp-quality >= 25.