|
|---|
|
|
|
|
|
|
g**********y
发帖数: 423 | 1 欢迎讨论，特别是各种程序的调用参数 。。。
http://dl.dropbox.com/u/62547840/NGS_Illumina.pm
http://dl.dropbox.com/u/62547840/NGS_Illumina.pl
screen output:
Illumina 1.3+ fastq format: ASCII(min, max) = (66, 102)
2012/08/25 11:41:15 START maq ill2sanger Run1_testicular-28T_lane2_read1_
sequence.txt Testis_T28_read1_sanger.fq
2012/08/25 11:42:57 SUCCESS after running 0 hours 1 minutes 42 seconds
2012/08/25 11:42:57 START maq ill2sanger Run1_testicular-28T_lane2_read2_
sequence.txt Testis_T28_read2_sanger.fq
2012/08/25 11:44:37 SUCCESS after running 0 hours 1 minutes 40 seconds
2012/08/25 11:44:37 START fastx_quality_stats -Q 33 -i Testis_T28_read1_
sanger.fq -o ./qcstats/Testis_T28_read1_sanger.fq_stats.txt
2012/08/25 11:49:13 SUCCESS after running 0 hours 4 minutes 36 seconds
2012/08/25 11:49:13 START fastq_quality_boxplot_graph.sh -i ./qcstats/Testis
_T28_read1_sanger.fq_stats.txt -o ./qcstats/Testis_T28_read1_sanger.fq_stats
.png -t "Testis_T28_read1_sanger.fq"
2012/08/25 11:49:13 SUCCESS after running 0 hours 0 minutes 0 seconds
2012/08/25 11:49:13 START fastx_quality_stats -Q 33 -i Testis_T28_read2_
sanger.fq -o ./qcstats/Testis_T28_read2_sanger.fq_stats.txt
2012/08/25 11:53:51 SUCCESS after running 0 hours 4 minutes 38 seconds
2012/08/25 11:53:51 START fastq_quality_boxplot_graph.sh -i ./qcstats/Testis
_T28_read2_sanger.fq_stats.txt -o ./qcstats/Testis_T28_read2_sanger.fq_stats
.png -t "Testis_T28_read2_sanger.fq"
2012/08/25 11:53:51 SUCCESS after running 0 hours 0 minutes 0 seconds
2012/08/25 11:53:51 START bwa aln -t 8 /data/public/reference_genomes/genome
_hg18.fa Testis_T28_read1_sanger.fq > ./bam/Testis_T28.read1.sai
2012/08/25 12:42:44 SUCCESS after running 0 hours 48 minutes 53 seconds
2012/08/25 12:42:44 START bwa aln -t 8 /data/public/reference_genomes/genome
_hg18.fa Testis_T28_read2_sanger.fq > ./bam/Testis_T28.read2.sai
2012/08/25 13:33:10 SUCCESS after running 0 hours 50 minutes 26 seconds
2012/08/25 13:33:10 START bwa sampe /data/public/reference_genomes/genome_
hg18.fa ./bam/Testis_T28.read1.sai ./bam/Testis_T28.read2.sai Testis_T28_
read1_sanger.fq Testis_T28_read2_sanger.fq > ./bam/Testis_T28.sam
2012/08/25 13:50:34 SUCCESS after running 0 hours 17 minutes 24 seconds
2012/08/25 13:50:34 START samtools import /data/public/reference_genomes/
genome_hg18.fa.fai ./bam/Testis_T28.sam ./bam/Testis_T28.bam
2012/08/25 14:03:10 SUCCESS after running 0 hours 12 minutes 36 seconds
2012/08/25 14:03:10 START samtools sort ./bam/Testis_T28.bam ./bam/Testis_
T28.sorted
2012/08/25 14:25:58 SUCCESS after running 0 hours 22 minutes 48 seconds
2012/08/25 14:25:58 START samtools index ./bam/Testis_T28.sorted.bam
2012/08/25 14:26:42 SUCCESS after running 0 hours 0 minutes 44 seconds
2012/08/25 14:26:42 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.
44/MarkDuplicates.jar VALIDATION_STRINGENCY=SILENT M=PCR_duplicates.M.txt
REMOVE_DUPLICATES=true AS=true I=./bam/Testis_T28.sorted.bam O=./bam/Testis_
T28.sorted.rmdup.bam
2012/08/25 14:40:45 SUCCESS after running 0 hours 14 minutes 3 seconds
2012/08/25 14:40:45 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.
44/AddOrReplaceReadGroups.jar RGID=lane1 RGLB=Testis_T28.fastq RGPL=Illumina
RGPU=run RGSM=Testis_T28 CREATE_INDEX=TRUE VALIDATION_STRINGENCY=SILENT I=.
/bam/Testis_T28.sorted.rmdup.bam O=./bam/Testis_T28.sorted.rmdup.rg.bam
2012/08/25 14:52:13 SUCCESS after running 0 hours 11 minutes 28 seconds
2012/08/25 14:52:13 START samtools index ./bam/Testis_T28.sorted.rmdup.rg.
bam
2012/08/25 14:52:59 SUCCESS after running 0 hours 0 minutes 46 seconds
2012/08/25 14:53:00 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T
RealignerTargetCreator -l INFO -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod
-R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.sorted
.rmdup.rg.bam -o ./snp_analysis_gatk/Testis_T28.intervals > ./log/Testis_T28
.intervals.log
2012/08/25 16:29:57 SUCCESS after running 1 hours 36 minutes 57 seconds
2012/08/25 16:29:57 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T IndelRealigner -
l INFO -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/
reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.sorted.rmdup.rg.bam -
targetIntervals ./snp_analysis_gatk/Testis_T28.intervals -o ./bam/Testis_T28
.realigned.bam -stats ./bam/Testis_T28.realign.stats.txt > ./log/Testis_T28.
realign.log
2012/08/26 00:40:15 SUCCESS after running 8 hours 10 minutes 18 seconds
2012/08/26 00:40:15 START samtools index ./bam/Testis_T28.realigned.bam
2012/08/26 00:41:08 SUCCESS after running 0 hours 0 minutes 53 seconds
2012/08/26 00:41:08 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.
44/SortSam.jar SO=coordinate VALIDATION_STRINGENCY=SILENT I=./bam/Testis_T28
.realigned.bam O=./bam/Testis_T28.realigned.sorted.bam
2012/08/26 00:52:36 SUCCESS after running 0 hours 11 minutes 28 seconds
2012/08/26 00:52:36 START samtools index ./bam/Testis_T28.realigned.sorted.
bam
2012/08/26 00:53:21 SUCCESS after running 0 hours 0 minutes 45 seconds
2012/08/26 00:53:21 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /home
/gmslz/tools/picard-tools-1.44/FixMateInformation.jar SO=coordinate
VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=2000000 I=./bam/Testis_T28.
realigned.sorted.bam O=./bam/Testis_T28.realigned.sorted.fixed.bam
2012/08/26 01:14:28 SUCCESS after running 0 hours 21 minutes 7 seconds
2012/08/26 01:14:28 START samtools index ./bam/Testis_T28.realigned.sorted.
fixed.bam
2012/08/26 01:15:13 SUCCESS after running 0 hours 0 minutes 45 seconds
2012/08/26 01:15:13 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T CountCovariates
-l INFO -nt 8 --downsample_to_coverage 10000 --default_platform Illumina -
cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov
DinucCovariate -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public
/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.realigned.sorted.fixed
.bam -recalFile ./snp_analysis_gatk/Testis_T28.recal.csv > ./log/Testis_T28.
count.covariates.log
2012/08/26 01:25:00 SUCCESS after running 0 hours 9 minutes 47 seconds
2012/08/26 01:25:00 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T
TableRecalibration -l INFO --default_platform Illumina -R /data/public/
reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.realigned.sorted.fixed.
bam -recalFile ./snp_analysis_gatk/Testis_T28.recal.csv --out ./bam/Testis_
T28.final.recalibrated.bam > ./log/Testis_T28.recalibration.log
2012/08/26 02:00:22 SUCCESS after running 0 hours 35 minutes 22 seconds
2012/08/26 02:00:22 START samtools index ./bam/Testis_T28.final.recalibrated
.bam
2012/08/26 02:01:27 SUCCESS after running 0 hours 1 minutes 5 seconds
2012/08/26 02:01:27 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T IndelGenotyperV2
-l INFO --window_size 450 -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R
/data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.final.
recalibrated.bam -o ./snp_analysis_gatk/Testis_T28.indels.vcf -bed ./snp_
analysis_gatk/Testis_T28.indels.bed > ./log/Testis_T28.indels.log
2012/08/26 02:40:46 SUCCESS after running 0 hours 39 minutes 19 seconds
2012/08/26 02:40:46 START python /data/public/tools/gatk-v4333/Sting/python/
makeIndelMask.py ./snp_analysis_gatk/Testis_T28.indels.bed 10 ./snp_analysis
_gatk/Testis_T28.indels.mask.bed
2012/08/26 02:40:46 SUCCESS after running 0 hours 0 minutes 0 seconds
2012/08/26 02:40:46 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T UnifiedGenotyper
-l INFO -stand_call_conf 30 -stand_emit_conf 10 -pl SOLEXA -mmq 30 -mm40 3
-D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_
genomes/genome_hg18.fa -I ./bam/Testis_T28.final.recalibrated.bam -o ./snp_
analysis_gatk/Testis_T28.raw.snps.vcf > ./log/Testis_T28.snp.log
2012/08/26 04:48:58 SUCCESS after running 2 hours 8 minutes 12 seconds
2012/08/26 04:48:58 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data
/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T
VariantFiltration -l INFO --clusterSize 3 --clusterWindowSize 10 --
filterExpression "DP <= 8" --filterName "DP8" --filterExpression "SB > -0.10
" --filterName "StrandBias" --filterExpression "HRun > 8" --filterName "
HRun8" --filterExpression "QD < 5.0" --filterName "QD5" --filterExpression "
MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" --filterName "hard2validate" -D /
data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_genomes/
genome_hg18.fa -B:variant,VCF ./snp_analysis_gatk/Testis_T28.raw.snps.vcf -B
:mask,Bed ./snp_analysis_gatk/Testis_T28.indels.mask.bed --maskName InDel -o
./snp_analysis_gatk/Testis_T28.snp.filtered.vcf > ./log/Testis_T28.snp.
filter.log
2012/08/26 04:53:29 SUCCESS after running 0 hours 4 minutes 31 seconds | k****x
发帖数: 265 | | B****m
发帖数: 63 | 3 perl果然很强大，以前用过bash把各个模块串起来。个人感觉最难的是下游的生物学解
释。 | b******y
发帖数: 627 | 4 I thought I knew how to use perl. Now I know that I am not even close.
Thanks for sharing. | e*******o
发帖数: 4654 | 5
many scientists using the old Perl as ten years ago.
http://onyxneon.com/books/modern_perl/
【在 b******y 的大作中提到】
: I thought I knew how to use perl. Now I know that I am not even close.
: Thanks for sharing.
|
|
|
|
|
|
|
|
