User:Lindenb/Notebook/UMR915/20101118

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Contents

Integragen

creating custom reports for Cedric

genome index

with w=10 and n=100000

Found >chr10 (overflows: 0 keys:0 time=0mins)
Found >chr10_random (overflows: 0 keys:914598 time=3mins)
Found >chr11 (overflows: 0 keys:914688 time=3mins)
Found >chr11_random (overflows: 0 keys:981628 time=10mins)
Found >chr12 (overflows: 0 keys:981674 time=10mins)
Found >chr13 (overflows: 0 keys:1005805 time=18mins)
Found >chr13_random (overflows: 0 keys:1014564 time=25mins)
Found >chr14 (overflows: 0 keys:1014594 time=25mins)
Found >chr15 (overflows: 0 keys:1020981 time=34mins)
Found >chr15_random (overflows: 0 keys:1025636 time=43mins)
Found >chr16 (overflows: 0 keys:1025676 time=43mins)
Found >chr16_random (overflows: 0 keys:1030318 time=52mins)
Found >chr17 (overflows: 0 keys:1030330 time=53mins)
Found >chr17_random (overflows: 0 keys:1033787 time=64mins)
Found >chr18 (overflows: 0 keys:1033893 time=64mins)
Found >chr18_random (overflows: 0 keys:1035503 time=74mins)
Found >chr19 (overflows: 0 keys:1035503 time=74mins)
Found >chr19_random (overflows: 17748 keys:1037703 time=85mins)
Found >chr1 (overflows: 17757 keys:1037710 time=85mins)
Found >chr1_random (overflows: 67020 keys:1040612 time=114mins)
Found >chr20 (overflows: 67329 keys:1040639 time=114mins)
Found >chr21 (overflows: 80664 keys:1041395 time=122mins)
Found >chr21_random (overflows: 87230 keys:1041728 time=127mins)
Found >chr22 (overflows: 87390 keys:1041741 time=127mins)
Found >chr22_random (overflows: 97502 keys:1042225 time=134mins)
Found >chr2 (overflows: 97546 keys:1042225 time=134mins)
Found >chr2_random (overflows: 143488 keys:1043649 time=174mins)
Found >chr3 (overflows: 143550 keys:1043653 time=175mins)
Found >chr3_random (overflows: 180767 keys:1044438 time=212mins)
Found >chr4 (overflows: 180828 keys:1044440 time=212mins)
Found >chr4_random (overflows: 212465 keys:1045050 time=249mins)
Found >chr5 (overflows: 212538 keys:1045056 time=250mins)
Found >chr5_random (overflows: 245394 keys:1045585 time=283mins)
Found >chr6 (overflows: 245412 keys:1045586 time=283mins)
Found >chr6_random (overflows: 277232 keys:1046030 time=325mins)
Found >chr7 (overflows: 277466 keys:1046044 time=325mins)
Found >chr7_random (overflows: 311231 keys:1046424 time=366mins)
Found >chr8 (overflows: 311286 keys:1046428 time=366mins)
Found >chr8_random (overflows: 337798 keys:1046667 time=400mins)
Found >chr9 (overflows: 337888 keys:1046670 time=400mins)

Found >chrM (overflows: 363584 keys:1046890 time=435mins) Found >chrX (overflows: 363584 keys:1046891 time=435mins) Found >chrX_random (overflows: 389846 keys:1047053 time=481mins) Found >chrY (overflows: 390188 keys:1047060 time=482mins) overflows: 394766 keys: 1047086 time=488mins

 du -h bdb/
 2.9G	bdb/

Samtools

updating samtools-0.1.10.tar.bz2 (prev version was 1.7 )

Belgium

MosaikSort -in align1.mka -out align1.sorted.mka
MosaikText -in align1.sorted.mka  -bam jeter.bam

samtools-0.1.10/samtools index jeter.bam
java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa -I jeter.bam  -o snps.raw.vcf   -D /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_129_hg18.rod -stand_call_conf 50.0 -stand_emit_conf 10.0  -dcov 50 > jeter.vcf

hum.. it doesn't count the INDELS

 java -jar GenomeAnalysisTK.jar -T IndelGenotyperV2 -l INFO  -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa -I jeter.bam  -o jeter.indel.vcf -O jeter2.out

erreur


IGV

downloaded IGV . It runs badly behind our firewall: http://www.broadinstitute.org/igv/home

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