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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

CombineGVCFs with error output

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    Yifei Sun

    What I done before combine:

    BWA-samtools-markduplicate(MarkDuplicates+SortSam+index)-realign(AddOrReplaceReadGroups+index+RealignerTargetCreator+IndelRealigner)-genotypecalling(HaplotypeCaller)

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    Gökalp Çelik

    Hi Yifei Sun

    You seem to have combined your gvcf files but you have not genotyped them yet. You need to use GenotypeGVCFs to get your variant sites in your vcf file. Do you have any other issue that makes you think this output is not correct ?

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    Yifei Sun

    Dear Gökalp Çelik

    Thank you for your reply. In fact, I found that in AddOrReplaceReadGroups step, I typed the SM=whatever, which cause all vcf i got had the same column name, and I propose this is the key error?

    PS: Do you mean I need to first GenotypeGVCFs on my each vcf file, then combine them?

    Thank you very much!!

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    Gökalp Çelik

    Hi Yifei Sun

    Sample names must be unique so if you have set all the samplenames as whatever you need to replace them before haplotypecaller step. Also after combining your GVCF files you need to genotype them to get variant sites. 

     

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    Yifei Sun

    Dear Gökalp Çelik

    Thank you for you reply!!

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