Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Rocketknight indeed I didn't want indels, but now I need it. Do you know which option should I use to obtain a final file with SNPs and Indels?
-
Is the order of funtions important?
Does this:
Code:FixMateInformation SortSam MarkDuplicates RealignerTargetCreator IndelRealigner
Code:SortSam FixMateInformation RealignerTargetCreator IndelRealigner MarkDuplicates
Leave a comment:
-
The Mills and 1000G gold standard indels are a very stringently curated list of indels. For the purposes of indel realignment in GATK you probably want one or more of the broader sets from the GATK bundle instead, though which ones I'm not completely sure.
Overall though, your workflow looks fine. Bear in mind though, that it will only call SNPs and not indels (but since you're calling your output file resultSNPs I assume you know that already).
Leave a comment:
-
GATK SNP calling complete workflow
Hi All,
I wolud like to consult my GATK workflow for a pair end Illumina data.
Generally I'm calling SNPs using following steps:
Code:bwa aln -t 4 hg19.fa seq1.fastq > 1.sai bwa aln -t 4 hg19.fa seq2.fastq > 2.sai bwa sampe -r "@RG\tID:exomeID\tLB:exomeLB\tSM:exomeSM\tPL:illumina\tPU:exomePU" hg19.fa 1.sai 2.sai seq1.fastq seq2.fastq > original.sam java -Xmx5g -jar FixMateInformation.jar I=original.sam O=fixed.sam SO=coordinate VALIDATION_STRINGENCY=LENIENT java -Xmx5g -jar SortSam.jar I=fixed.sam SO=coordinate O=first.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true java -Xmx5g -jar MarkDuplicates.jar I=first.bam O=marked.bam METRICS_FILE=metricsFile CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T RealignerTargetCreator -R hg19.fa -o intervalsList -I marked.bam -known Mills_and_1000G_gold_standard.indels.hg19.vcf java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T IndelRealigner -R hg19.fa -I marked.bam -targetIntervals intervalsList -known Mills_and_1000G_gold_standard.indels.hg19.vcf -o realigned.bam java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T CountCovariates -l INFO -R hg19.fa -I realigned.bam -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile recalFile -knownSites dbsnp_135.hg19.vcf java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T TableRecalibration -R hg19.fa -I realigned.bam -o recalibrated.bam -recalFile recalFile java -Xmx5g -jar GenomeAnalysisTK.jar -nt 4 -T UnifiedGenotyper -R hg19.fa -I recalibrated.bam -o resultSNPs.vcf -D dbsnp_135.hg19.vcf -metrics UniGenMetrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A DepthOfCoverage -A AlleleBalance -L exomes.bed
The exome intervals I've gained using UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?command=start
I'm not sure if I'm doing it in a correct way. Is my way compact enough? What about yours workflows? Are your steps look simillar? Should I use more GATK subprograms to obtain more accurate results?
Thanks in advance for suggestionsTags: None
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...-
Channel: Articles
Yesterday, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
45 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Leave a comment: