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Different coverage metrics between GATK and PICARD
Hi all, I want to evaluate the panel performance by calculating the target coverage. Both GATK and PICARD offered great convenience for the calculation. However, slightly difference was observed. And...
View Articlegatk 3.6 MIN_DP much lower then DP
I'm analysing a set of bacterial isolates, some which are (almost) identical to the reference, and some which are very different. Despite the fact that the identical isolates have good coverage (80x),...
View Articleerror with GenotypeGVCFs
commands are: java -Xmx10g -jar $gatk -T HaplotypeCaller \ -R $refGenome \ --dbsnp $dbSNP \ -o s1.raw.var.g.vcf.gz \ -I s1.bam \ -pairHMM VECTOR_LOGLESS_CACHING \ --emitRefConfidence GVCF...
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(How to) Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
This tutorial updates Tutorial#2799. Here we discuss two tools, MarkDuplicates and MarkDuplicatesWithMateCigar, that flag duplicates. We provide example data and example commands for you to follow...
View ArticleHigh proportion of spanning deletion in a whole-genome callset
Hi GATK team, I am working on a callset of ~150 high coverage human genomes. My processing pipeline follows the GATK Best Practices except that 1-I use IndelRealigner because we started processing the...
View ArticlePicard liftover from build 38 to 37 fails on alternate contigs
I am trying to lift a VCF from build 38 to build 37 using Picard liftover. I'm using this chain file: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz I get this error:...
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Variant reported by GATK is not seen in IGV
I am facing an issue with GATK 3.8. After running GATK HaplotypeCaller I get one variant detected as Pf3D7_05_v3 133207 . A G 60 ....
View ArticleThe mean of fields in BQSR table file
Hi I am not very clear about fields in BQSR table file(like errors,EmpiricalQuality...).I have tried finding answers,but the result is not very ideal.Could you give me some advice? Thanks, Ruler
View Articlehg38 version
Hello! I have found in your cloud bundle (https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/) the reference fasta of the hg 38...
View ArticleHaplotypeCaller does not filter duplicate reads, why?
Hi, Im running HaplotypeCaller on a server this way: java -XX:ParallelGCThreads=8 -Xmx80g -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -I a2tl1_14_final.bam --min_base_quality_score 25...
View ArticleWhy does GenotypeGVCF add duplicated SNPs past the end of the GVCF region?
I ran HaplotypeCaller per sample on the entire genome, then merged multiple samples together into the same GVCF using CombineGVCFs. The CombineGVCFs step was run with -L to split up the GVCFs into...
View ArticleUse vcf from HaplotypeCaller as normal_panel with Mutect2 (GAKT4.beta.6) ?
Hi, I am trying to find somatic mutations in blood samples. The same samples were used previously to detect germline variants with HaplotypeCaller. Does it make sense to use the vcf obtained for a...
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(How to) Run FlagStatSpark on a cloud Spark cluster
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. It may take a minute or a...
View ArticleWhy does SelectVariants discard variants when the input vcf is unsorted?
I am using SelectVariants to subset based on samples, while trying to keep all variants. However, SelectVariants seems to discard variants when the input file is not sorted and an index file is...
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Potential ploidy problem in GenotypeGVCFS
Dear Geraldine, Sheila and GATK community, I am trying to run GenotypeGVCFs on set of 90 individuals; they range in ploidy (between 2 and 5). I didn't do MQ filtering on my bams (I have fairly short...
View ArticleBCL to uBAM tutorial update
Hi there, I'm very interested on try the BCL to uBAM protocol (Tutorial#6570 coming soon) you have mentioned on your article #6483 ((How to) Map and clean up short read sequence data efficiently). Do...
View ArticleWatch Live ##Toronto Raptors VS Boston Celtics 12 November 2017 Online
Watch Live ##Toronto Raptors VS Boston Celtics 12 November 2017 Online ? PLAY NOW ? http://bit.ly/2Aq2Y8v ? Download Now ? http://bit.ly/2Aq2Y8v ? Watch Now ? http://bit.ly/2Aq2Y8v ? Final Watch ?...
View ArticleBAM with soft-clipped primer sequences as an input for RevertSam (Tutorial...
Could I use RevertSam on primer-clipped BAM and then MergeBamAlignment using the primer-clipped BAM and uBAM originated from it as input? I'm analyzing paired-end TruSeq Custom Amplicon panel data,...
View ArticleGATK v3.8 install
hello,I install the GATK 3.8,and then give me it : # tar: Ignoring unknown extended header keyword LIBARCHIVE.creationtime' tar: Ignoring unknown extended header keyword SCHILY.dev' tar: Ignoring...
View ArticlePE mates are lost while downsampling with -dfrac?
Hi GATK team and users, I am using PrintReads with -dfrac option to simulate different depths of coverage. The original data contains WGS, PE reads (from GATK's Bundle bam, PrintReads with -L 20,...
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