GDC Callers

3 Aug 2017

20 July 2017

22 June 2017

Currently ~48 hours running "training" of JointSNVMix against IS3 (diploid)

Need to compile MutationSeq

Started downloading AML data from SRA yesterday

8 June 2017

training somaticseq

emailed dbsnp

25 May 2017

MB data from ICGC available with CLL?

COLO829 bams available in the new dataset? includes AML?

17 May 2017

11 May 2017

tictac repo branches

tictac repo http://128.231.12.18/deaconjs/tictac

Create GDC & SomaticSeq branches?

Pipeline Notes

SomaticSeq publication classifiers do not appear to be available.

Comparing parallel runs with single thread using interval and ignore regions

somaticseq results 11May

parallel somaticseq call on interval 102

. /etc/profile.d/modules.sh; module load python3/3.5.1; pip install --user regex numpy scipy pysam

module load bedtools python3/3.5.1; module load jdk/1.8.0_111; module load R/3.3.0;

/DCEG/Scimentis/tools2/somaticseq/SomaticSeq.Wrapper.sh \

--mutect callers/mutect/is4/results/combined.mutect.is4.102.vcf \

--varscan-snv callers/varscan2/is4/results/combined.varscan2.is4.102.vcf.snp.vcf \

--varscan-indel callers/varscan2/is4/results/combined.varscan2.is4.102.vcf.indel.vcf \

--sniper callers/sniper/is4/results/combined.sniper.is4.102.vcf \

--muse callers/muse/is4/results/combined.muse.is4.102.vcf \

--normal-bam synthetic.challenge.set4.normal.bam \

--tumor-bam synthetic.challenge.set4.tumour.bam \

--genome-reference human_g1k_v37_decoy.fasta \

--cosmic reference/dbs/b37_cosmic_v54_120711.vcf \

--dbsnp dbs/dbsnp_132_b37.leftAligned.vcf.gz \

--inclusion-region reference/bedfiles/102.bed \

--gatk /DCEG/Scimentis/tools2/gatk/GenomeAnalysisTK.jar \

--output-dir callers/somaticseq/is4/results/102.vcf \

--ada-r-script somaticseq/r_scripts/ada_model_predictor.R \

--classifier-snv reference/somaticseq/training/is3/Ensemble.sSNV.tsv.ntChange.Classifier.RData \

--pass-threshold 0.5 \

--lowqual-threshold 0.1

wg call

The sorted.chr files are sorted then filtered all reads except labels 1-22

. /etc/profile.d/modules.sh; module load python3/3.5.1; \

pip install --user regex numpy scipy pysam; module load bedtools python3/3.5.1 jdk/1.8.0_111 R/3.3.0; \

SomaticSeq.Wrapper.sh \

--mutect callers/mutect/is4/final/merged.mutect.is4.sorted.chr.vcf.recode.vcf \

--varscan-snv callers/varscan2/is4/final/merged.varscan2.is4.snp.sorted.chr.vcf.recode.vcf \

--varscan-indel callers/varscan2/is4/final/merged.varscan2.is4.indel.sorted.chr.vcf.recode.vcf \

--sniper callers/sniper/is4/final/merged.sniper.is4.sorted.chr.vcf.recode.vcf \

--muse callers/muse/is4/final/merged.muse.is4.sorted.chr.vcf \

--normal-bam synthetic.challenge.set4.normal.bam \

--tumor-bam synthetic.challenge.set4.tumour.bam \

--genome-reference human_g1k_v37_decoy.fasta \

--cosmic b37_cosmic_v54_120711.vcf \

--dbsnp dbsnp_132_b37.leftAligned.vcf.gz \

--gatk GenomeAnalysisTK.jar \

--output-dir wg.somaticseq.is4.ignore.vcf \

--ada-r-script somaticseq/r_scripts/ada_model_predictor.R \

--classifier-snv somaticseq/training/is3/Ensemble.sSNV.tsv.ntChange.Classifier.RData \

--pass-threshold 0.5 \

--lowqual-threshold 0.1 \

--exclusion-region wg.somaticseq.nox.ignore.bed

3 May 2017

GDC_pipeline_results.xlsx

25 April 2017

18 April 2017

13 April 2017

GDC Callers Results

sh  |bam vcf mpil merged |r qw |pipeline

------------------------------------------------------------------

666 |666 0   0   0       |0   0 |benchmarks/is1/intervals

333 |0   0   333 0       |0   0 |benchmarks/is1/mpileups

666 |666 0   0   0       |0   0 |benchmarks/is2/intervals

333 |0   0   106 0       |106 0 |benchmarks/is2/mpileups

666 |666 0   0   0       |0   0 |benchmarks/is4/intervals

333 |0   0   333 0       |0   0 |benchmarks/is4/mpileups

666 |666 0   0   0       |0   0 |benchmarks/is3/intervals

333 |0   0   333 0       |0   0 |benchmarks/is3/mpileups

333 |0   426 0   1       |0   0 |callers/muse/is1

333 |0   290 0   0       |0   0 |callers/muse/is2

333 |0   876 0   1       |0   0 |callers/muse/is3

333 |0   864 0   1       |0   0 |callers/muse/is4

333 |0   152 0   0       |40  0 |callers/sniper/is1

333 |0   59  0   0       |59  0 |callers/sniper/is2

333 |0   999 0   1       |0   0 |callers/sniper/is3

333 |0   999 0   1       |0   0 |callers/sniper/is4

333 |0   999 0   1       |0   0 |callers/mutect/is1

333 |0   661 0   0       |5   0 |callers/mutect/is2

333 |0  1332 0   1       |0   0 |callers/mutect/is3

333 |0  1332 0   1       |0   0 |callers/mutect/is4

333 |0  2664 0   1       |0   0 |callers/varscan2/is3

333 |0   650 0   0       |0   0 |callers/varscan2/is4

30 March 2017

muse (bed file option)

    cmdstr += "$BINDIR/MuSEv1.0rc_submission_b391201 "

    cmdstr += "call "

    cmdstr += "-l %s/variant_calling_bed.%s.bed "%(bedsloc, region+1)

    cmdstr += "-O $OUTDIR/muse.is3.%s "%(region+1)

    cmdstr += "-f $REFDIR/human_g1k_v37_decoy.fasta "

    cmdstr += "$DATADIR/synthetic.challenge.set3.tumor.bam "

    cmdstr += "$DATADIR/synthetic.challenge.set3.normal.bam "

    cmdstr += "\n"

    outlines.append(cmdstr)

    cmdstr = ""

    cmdstr += "$BINDIR/MuSEv1.0rc_submission_b391201 "

    cmdstr += "sump "

    cmdstr += "-I $OUTDIR/muse.is3.%s.MuSE.txt "%(region+1)

    cmdstr += "-G "

    cmdstr += "-O $OUTDIR/muse.is3.%s.vcf "%(region+1)

    cmdstr += "-D $DBDIR/dbsnp_db/$DBSNP "

chr19

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

840 4 844 0 861 0

sensitivity, specificity, balanced accuracy: 0.975,0.995,0.985

is3

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

5615 198 5813 2869 6391 1512

sensitivity, specificity, balanced accuracy: 0.878,0.965,0.922

last meeting

mutect (bed file option)

    cmdstr += "$JAVADIR/java -Xmx4g -jar $BINDIR/mutect-1.1.7.jar "

    cmdstr += "--analysis_type MuTect "

    cmdstr += "--reference_sequence $REFDIR/human_g1k_v37_decoy.fasta "

    cmdstr += "--cosmic $DBDIR/cosmic_db/b37_cosmic_v54_120711.vcf "

    cmdstr += "--dbsnp $DBDIR/dbsnp_db/dbsnp_132_b37.leftAligned.vcf.gz "

    cmdstr += "--input_file:normal $DATADIR/synthetic.challenge.set3.normal.bam "

    cmdstr += "--input_file:tumor $DATADIR/synthetic.challenge.set3.tumor.bam "

    cmdstr += "--out $OUTDIR/mutect.is3.%s.out "%(region+1)

    cmdstr += "--vcf $OUTDIR/mutect.is3.%s.vcf "%(region+1)

    cmdstr += "--enable_qscore_output "

    cmdstr += "--intervals %s/variant_calling_bed.%s.bed "%(bedsloc, region+1)

chr19

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

841 50 891 0 861 0

sensitivity, specificity, balanced accuracy: 0.976,0.943,0.960

is3

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

5952 2135 8087 924607 6391 1512

sensitivity, specificity, balanced accuracy: 0.931,0.735,0.833

sniper (bamsplit)

    cmdstr += "$BINDIR/somatic-sniper-1.0.4/build/bin/bam-somaticsniper "

    cmdstr += "-f $REFDIR/human_g1k_v37_decoy.fasta "

    cmdstr += "$DATADIR/tumor.is3.%s.bam.gz "%(region+1)

    cmdstr += "$DATADIR/normal.is3.%s.bam.gz "%(region+1)

    cmdstr += "$OUTDIR/%s.is3.%s.vcf "%(caller, region+1)

    cmdstr += "-J "

    cmdstr += "-F vcf "

    # recommended by authors

    cmdstr += "-G -L "

    cmdstr += "-Q 40 -q 1 "

chr19

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

770 112 882 0 861 0

sensitivity, specificity, balanced accuracy: 0.894,0.873,0.883

is3

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

5379 4736 10115 2590 6391 1512

sensitivity, specificity, balanced accuracy: 0.841,0.531,0.686

varscan2 (bamsplit->mpileups)

java -jar $BINDIR/varscan/VarScan.v2.3.6.jar

somatic

$DATADIR/chr19.normal-tumor.mpileup

$OUTDIR/varscan2.chr19.mvf02

--output-vcf

--mpileup 1

--min-var-freq 0.02

--strand-filter 1

--minimum-coverage 6

chr19

tpcount, fpcount, subrecs, submasked, trurecs, trumasked:

835 75329 76164 0 861 0

sensitivity, specificity, balanced accuracy: 0.969,0.010,0.490

is3

not complete (pileups running, may have to mpileup regions)

bamsplit (split a bam file into regions)

cmd = "bedtools intersect -sorted -g %s -b %s -abam %s > %s\n"%(genomefile, bedname, bamstosplit[bamindex], interval_bamname)

mpileups (per region)

            cmd = "samtools mpileup -f $REFDIR/human_g1k_v37_decoy.fasta "

            cmd += "-q 1 -A -B -Q 13 "

            cmd += "-l %s/variant_calling_bed.%s.bed "%(bedbase, x+1)

            cmd += "%s/synthetic.challenge.set3.normal.bam "%(bambase)

            cmd += "%s/synthetic.challenge.set3.tumor.bam "%(bambase)

            cmd += " > %s/mpileups/results/%s.is3.%s.mpileup "%(benchbase, bamindex, x+1)

Report abuse