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
fastq_quality_boxplot_graph.sh -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
fastq_quality_boxplot_graph.sh -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
