User:Lindenb/Notebook/UMR915/20101124

Cover
waiting for http://www.cell.com/immunity/home ...

Sysadmin
meeting with SC : we need space

Dindel
installing dindel from sources http://www.sanger.ac.uk/resources/software/dindel. Edit the Makefile and set the path to the samtools src then 'make'. g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o DInDel.o DInDel.cpp Library.hpp: In member function ‘void Library::calcProb(const std::vector&)’: Library.hpp:89: warning: converting to ‘int’ from ‘const double’ g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o HapBlock.o HapBlock.cpp g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o HaplotypeDistribution.o HaplotypeDistribution.cpp g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o ObservationModelFB.o ObservationModelFB.cpp Library.hpp: In member function ‘void Library::calcProb(const std::vector&)’: Library.hpp:89: warning: converting to ‘int’ from ‘const double’ g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o GetCandidates.o GetCandidates.cpp Library.hpp: In member function ‘void Library::calcProb(const std::vector&)’: Library.hpp:89: warning: converting to ‘int’ from ‘const double’ g++ -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3  -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c -o Faster.o Faster.cpp Library.hpp: In member function ‘void Library::calcProb(const std::vector&)’: Library.hpp:89: warning: converting to ‘int’ from ‘const double’ g++ -o dindel -I/usr/local/package/samtools-0.1.10 -Iseqan_library/ -I./ -Wno-deprecated  -O3   DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o   -L/usr/local/package/samtools-0.1.10  -lbam -lz -lboost_program_options -static /usr/local/package/samtools-0.1.10/libbam.a(knetfile.o): In function `socket_connect': /home/lindenb/samtools-0.1.10/knetfile.c:99: warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

but [lindenb@srv-clc-02]$ /usr/local/package/dindel-1.01-src/dindel --analysis getCIGARindels --bamFile sampe.sorted.bam --outputFile dindel_output  --ref mygene.fa Error parsing input options. Usage: (...) fixed the bug by changing "bamFiles" to "bamList" in /usr/local/package/dindel-1.01-src/DInDel.cpp (seems to be a bug in BOOST http://lists.boost.org/Archives/boost/2006/01/98811.php ).

/usr/local/package/dindel-1.01-src/dindel --analysis getCIGARindels --bamFile sampe.sorted.bam --outputFile dindel_output  --ref mygene.fa Reading BAM file: sampe.sorted.bam Parsing indels from CIGAR strings... Library: dindel_default mean: 207.5 stddev: 40.9283 Wrote indels in CIGARS for target XXXXXXX to file dindel_output Wrote library insert sizes to dindel_output.libraries.txt done!

head dindel_output.libraries.txt 0 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 (...) but makeWindows.py described in the manual is not available in the sources... Hum switching to the binaries... ok, restart python /usr/local/package/dindel-1.01/dindel-1.01-python/makeWindows.py --inputVarFile dindel_output.variants.txt --windowFilePrefix sample.realign_windows --numWindowsPerFile 1000 (...) Number of candidates: 604 Number of windows: 494 Maximum window size: 161 Mean window size: 121 Chromosome: chr7_random Total lines: 173 at minimum distance 20 Number of candidates: 173 Number of windows: 131 Maximum window size: 141 Mean window size: 121 Chromosome: chrX_random Total lines: 200 at minimum distance 20 Number of candidates: 200 Number of windows: 163 Maximum window size: 141 Mean window size: 121 Chromosome: chr9 Total lines: 41545 at minimum distance 20 Number of candidates: 41545 Number of windows: 27168 Maximum window size: 848 Mean window size: 122 Chromosome: chr8 Total lines: 38569 at minimum distance 20 Number of candidates: 38569 Number of windows: 25891 Maximum window size: 201 Mean window size: 122 Chromosome: chr16_random Total lines: 12 at minimum distance 20 Number of candidates: 12 Number of windows: 10 Maximum window size: 123 Mean window size: 119 Chromosome: chr10 Total lines: 46560 at minimum distance 20 Number of candidates: 46560 Number of windows: 30113 Maximum window size: 321 Mean window size: 122 Chromosome: chr17_random Total lines: 763 at minimum distance 20 Number of candidates: 763 Number of windows: 587 Maximum window size: 161 Mean window size: 121 Many files are generated... Then for each result file one should /usr/local/package/dindel-1.01/binaries/dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile recal_bwa_rmdup_XXXX.bam --outputFile sample.dindels.1  --ref /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa --varFile sample.realign_windows.1.txt --libFile dindel_output.libraries.txt
 * 1) LIB dindel_default

head sample.dindels.1.glf.txt msg index analysis_type tid lpos rpos center_position realigned_position was_candidate_in_window ref_all nref_all num_reads post_prob_variant qual est_freq logZ hapfreqs indidx msq numOffAll num_indel num_cover_forward num_cover_reverse num_unmapped_realigned var_coverage_forward var_coverage_reverse nBQT nmmBQT mLogBQ nMMLeft nMMRight glf error_too_few_reads 1 NA chr6_random 417 536 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA error_too_few_reads 2 NA chr6_random 635 755 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA error_too_few_reads 3 NA chr6_random 2043 2162 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ok 4 dip.map chr6_random 5183 5302 5242 5243 1 NA +T 3 NA 0.0518175 NA NA NA 0 60 NA NA 1 0 0 1 0 NA NA NA NA NA 1/1:0.0518175 ok 4 dip chr6_random 5183 5302 5242 5243 1 NA +T,+TT 3 NA NA NA -21.4465 NA 0 60 0 0 1 0 0 1,0 0,0 129 1 -3.22403 0 0 0/0:-26.2281,0/1:-22.1231,0/2:-25.6365,1/1:-21.4403,1/2:-22.1099,2/2:-25.2702 ok 4 dip chr6_random 5183 5302 5242 5280 0 NA R=>A 3 NA NA NA -24.8196 NA 0 60 0 1 1 0 0 0 0 128 0 -3.22188 0 0 0/0:-26.2159,0/1:-25.4643,1/1:-24.8013 ok 5 dip.map chr6_random 21407 21538 21473 21467 1 NA +C 3 NA 0.000108848 NA NA NA 0 60 NA NA 1 1 0 0 0 NA NA NA NA NA 0/1:0.000108848 ok 5 dip chr6_random 21407 21538 21473 21467 1 NA +C 3 NA NA NA -17.8254 NA 0 53.4447 0 0 0 0 0 0 0 162 0 -3.27222 0 0 0/0:-17.8254,0/1:-19.2092,1/1:-34.9632 ok 5 dip chr6_random 21407 21538 21473 21468 1 NA +T 3 NA NA NA -17.8254 NA 0 53.4447 0 0 0 0 0 0 0 162 0 -3.27222 0 0 0/0:-17.8254,0/1:-19.2114,1/1:-35.423 save the file names: echo "sample.dindels.1.glf.txt" > sample.dindel_stage2_outputfiles.txt and then... python /usr/local/package/dindel-1.01/dindel-1.01-python/mergeOutputDiploid.py --inputFiles sample.dindel_stage2_outputfiles.txt --outputFile dindel.variants.vcf --ref /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa

Number of non-empty GLF files: 1 Calling variants from GLF file sample.dindels.1.glf.txt

more dindel.variants.vcf chrX_random	46862	. CTT	C	42	PASS	DP=2;NF=1;NR=1;NRS=1;NFS=1;HP=2	GT:GQ	1/1:6 chrX_random	49403	. g	gC	3	q20	DP=2;NF=1;NR=0;NRS=1;NFS=1;HP=1	GT:GQ	0/1:3 chrX_random	61565	. ga	g	49	PASS	DP=5;NF=1;NR=1;NRS=1;NFS=1;HP=2	GT:GQ	1/1:6 chrX_random	84517	. G	GA	9	q20	DP=2;NF=1;NR=1;NRS=1;NFS=1;HP=9	GT:GQ	1/1:6 chrX_random	149111	. c	cTG	11	q20	DP=4;NF=0;NR=1;NRS=0;NFS=1;HP=1	GT:GQ	1/1:4 chrX_random	1462787	. atg	a	59	PASS	DP=2;NF=1;NR=1;NRS=1;NFS=1;HP=1	GT:GQ	1/1:6 chrX_random	1468928	. A	AAG	11	q20	DP=3;NF=1;NR=1;NRS=2;NFS=1;HP=2	GT:GQ	1/1:6 chrX_random	1472124	. C	CGT	4	q20	DP=3;NF=0;NR=1;NRS=0;NFS=1;HP=1	GT:GQ	1/1:4
 * 1) fileformat=VCFv4.0
 * 2) source=Dindel
 * 3) reference=/GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa
 * 4) INFO=
 * 5) INFO=
 * 6) INFO=
 * 7) INFO=
 * 8) INFO=
 * 9) INFO=
 * 10) FORMAT=
 * 11) FORMAT=
 * 12) ALT=
 * 13) FILTER=
 * 14) FILTER=
 * 15) FILTER=
 * 16) FILTER=<ID=wv,Description="Other indel in window had higher likelihood">
 * 17) CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE

Cover for Immunity
http://www.cell.com/immunity/abstract/S1074-7613%2810%2900401-2 Cell-Cell Propagation of NF-κB Transcription Factor and MAP Kinase Activation Amplifies Innate Immunity against Bacterial Infection Immunity, Volume 33, Issue 5, 804-816, 18 November 2010. Christoph Alexander Kasper, Isabel Sorg, Christoph Schmutz, Therese Tschon, Harry Wischnewski, Man Lyang Kim, Cécile Arrieumerlou