Question: How to approach DNAseq
gravatar for xujiean66
4.1 years ago by
xujiean660 wrote:

hello,i am very grateful for your answers.Recently we make raw reads as chr22.fastq form NGS,then we want it to map to chr22.fa,then we have two other file for variant calling,contained SNPs.vcf and Indel.vcf,and we make out by lunix system,but we failed to find some tools in galaxy pane ,such as BaseRecalibrator and HaplotypeCaller ,so we dot know how to do next,the method was fllowing: the overstriking tools were not found in galaxy pane

fastx_quality_stats -i NA18489_chr22.fq -Q 33 -o fq_stats.text -i fq_stats.text -o out_quality.png -t "my libaray"

fastq_quality_filter -q 20 -p 75 -i NA18489_chr22.fq -Q 33 -o  NA18489_chr22_qf.fq

fastx_trimmer -f 2 -l 94 -i NA18489_chr22_qf.fq -Q 33 -o  NA18489_chr22_qf_tr.fq

fastx_quality_stats -i NA18489_chr22_qf_tr.fq -Q 33 -o fq_stats_qf_tr.text -i fq_stats _qf_tr.text -o out_quality_ qf_tr.png -t "my libaray"



bwa index -a bwtsw  chr22.fa

bwa aln chr22.fa  NA18489_chr22_qf_tr.fq > NA18489_chr22_aln.sai

bwa samse -r '@RG\tID:foo\tSM:bar\tLB:lib\tPL:illumina' chr22.fa NA18489_chr22_aln.sai NA18489_chr22_qf_tr.fq > NA18489_chr22_aln.sam



samtools view -b -S NA18489_chr22_aln.sam >  NA18489_chr22_aln.bam

samtools flagstat NA18489_chr22_aln.bam

samtools sort NA18489_chr22_aln.bam  NA18489_chr22_aln.sorted

java -jar /home/mib2014/software/picard-tools-1.119/picard-tools-1.119/MarkDuplicates.jar I=NA18489_chr22_aln.sorted.bam O=NA18489_chr22_dedup.bam METRICS_FILE= NA18489_chr22_dedup.metrics

samtools index NA18489_chr22_dedup.bam


samtools faidx chr22.fa

java -jar /home/mib2014/software/picard-tools-1.119/picard-tools-1.119/

CreateSequenceDictionary.jar  R=chr22.fa  O=chr22.dict



java -jar /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -T RealignerTargetCreator -R chr22.fa  -I  NA18489_chr22_dedup.bam -o NA18489_chr22.intervals -known indel_chr22_hg19.vcf


java -jar /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -I NA18489_chr22_dedup.bam -R chr22.fa -T IndelRealigner -targetIntervals NA18489_chr22.intervals -o NA18489_chr22_realn.bam -known indel_chr22_hg19.vcf


java -jar /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -T BaseRecalibrator -I  NA18489_chr22_realn.bam -R chr22.fa -knownSites  db138_chr22_hg19.vcf -o NA18489_chr22_recal.table


java -jar /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -T PrintReads -I NA18489_chr22_realn.bam -BQSR NA18489_chr22_recal.table -R chr22.fa -o NA18489_chr22_final.bam

java -jar /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -T HaplotypeCaller -R chr22.fa -I NA18489_chr22_final.bam -o NA18489_chr22.raw.snps.indels.vcf



java -jar  /home/mib2014/gatk-3.2/GenomeAnalysisTK.jar -T VariantFiltration -R chr22.fa --variant NA18489_chr22.raw.snps.indels.vcf -filterExpression "QUAL > 50" -filtername "filter" --mask db138_chr22_hg19.vcf -maskName snp




galaxy • 1.0k views
ADD COMMENTlink modified 4.1 years ago by Martin Čech ♦♦ 4.9k • written 4.1 years ago by xujiean660
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Please install any missing tools from your instance through the Tool Shed.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
gravatar for xujiean66
4.1 years ago by
xujiean660 wrote:

hello,if it can occur to left pane on Galaxy if i download them,or if i may be to use the cloud? Thanks.

ADD COMMENTlink written 4.1 years ago by xujiean660

I am sorry, but I do not quite understand what you are asking. If about where tools can be installed, your local or cloud Galaxy is the target instance. Then any jobs are run on that instance. Thanks, Jen, Galaxy team

ADD REPLYlink written 4.1 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour