User:Lindenb/Notebook/UMR915/20100618
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mysql
creating a table for the samples
create table sample(
id int unsigned primary key auto_increment,
name varchar(20) unique,
description text,
created datetime,
modified timestamp
);
SNP calling
filtering on depth( min/max) and Q: minimum RMS mapping quality for SNP
samtools pileup -vcf $(HG18) recal_bwa_rmdup_XXXX1.bam |\ samtools.pl varFilter -d 4 -D 1200 -Q 25 |\ java -jar ~/src/code915/dist/pileupfilter.jar -bed PCCR.bed | wc -l 43209 gunzip -c daily/20100601/for_pierre_010610/vcf_maq_pccr_changed_filters/XXXX1.vcf.gz | wc -l 35784
some filters are missing. OK, now just keep the single nucleotide mutations:
(...) | awk -F " " '{if(length($4)==1) print;}' | wc -l
37121
adding filter for the snp quality:
samtools pileup -vcf $(HG18) recal_bwa_rmdup_XXXX1.bam | samtools.pl varFilter -d 4 -D 1200 -Q 25 |\
java -jar ~/src/code915/dist/pileupfilter.jar -bed PCCR.bed -min-sq 25 |\
awk -F " " '{if(length($4)==1) print;}' > jeter.pileup
wc jeter.pileup
35286
comparison SS2/my data
comm -12: 34187 comm -13: 1569 (uniq to SS2 data) eg: 10:1036884,10:114049332 comm -23: 1099 (uniq to MY data) e.g: 10:101153184,10,101283025
 |  |
Comparaison Dindel/samtools
same as yesterday but remove non-PCCR from dindel (update: bug found in my src by SS2)
- count dindel :1492
- count samtools :3739
- uniq dindel :889
- uniq samtools :3136
- comm dindel/samtools :603
script was: sh 20100618.sh
cat ${HOME}/daily/20100604/XXXXX_variantCalls.VCF |\
grep -v "#" | awk -F ' ' '{if(length($5)!=1 && $7==".") print; }' |\
java -jar /home/lindenb/src/code915/dist/posfilter.jar -db XXX_0809_PCCR.bed |\
cut -d ' ' -f 1,2 | sort | uniq > jeter1.txt
cat ${HOME}/daily/20100528/indels_samtools_bwa/PCCR/XXXXXXsamtoolsIndel.vcf |\
grep -v "#" | awk -F ' ' '{if(length($5)!=1) print; }' |\
cut -d ' ' -f 1,2 | sort | uniq > jeter2.txt
echo -n "count dindel :"
wc -l jeter1.txt
echo -n "count samtools :"
wc -l jeter2.txt
echo -n "uniq dindel :"
comm --check-order -23 jeter1.txt jeter2.txt | wc -l
echo -n "uniq samtools :"
comm --check-order -13 jeter1.txt jeter2.txt | wc -l
echo -n "comm dindel/samtools :"
comm --check-order -12 jeter1.txt jeter2.txt | wc -l
rm jeter1.txt jeter2.txt
