Priyadarshini Thirunavukkarasu
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Activity overview
Latest activity by Priyadarshini Thirunavukkarasu-
Priyadarshini Thirunavukkarasu commented,
Hello By variances do you mean the variant allele?. There are variant alleles in the vcf
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Priyadarshini Thirunavukkarasu commented,
Hello These gvcf files were generated by the illumina software (miniseq) so not sure if it gzipped or end with an extension vcf.gz
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Priyadarshini Thirunavukkarasu commented,
Thank you. I removed the MNPs in all the gvcf files. This time, when I try to combine GVCFs, I get another error. The error shows the gvcf files are not gzipped. Please find the command and error m...
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Priyadarshini Thirunavukkarasu commented,
Thank you. In the truth data set downloaded from database, the contig position is given as chromosome number as Chr 1, Chr 2, Chr 3 and so on. In the filtered data set, the contigs are given as acc...
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Priyadarshini Thirunavukkarasu created a post,
Shared variants
AnsweredHello I have exome data sets from 6 individuals, in which 4 are affected and 2 are not affected. I have to identify the variants which are shared between the four affected individuals. I did the jo...
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Priyadarshini Thirunavukkarasu commented,
Thank you. So, the header of the filtered vcf data file and truth data vcf file should match?. If not, there are from different reference version. I will check the header of the vcf files. Is there...
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Priyadarshini Thirunavukkarasu commented,
Hello I used GRCh38 as reference genome for mapping the exome data and the truth data set was from genome in bottle datasets and was also annotated with GRCh38. So, it is not clear, why there is an...
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Priyadarshini Thirunavukkarasu commented,
Hello Sorry for the confusion. I am trying to evaluate the filtered variants in filtered vcf with truth data set. The truth data vcf fies has chromosome number as chr. But, the filtered vcf has ac...
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Priyadarshini Thirunavukkarasu created a post,
Replace chromosome (Chr) with accession number in the vcf header
Hello I am trying to validate filtered vcf with truth data set. The truth data vcf file and filtered vcf files have different headers which leads to the below error. The vcf files (filtered vcf da...
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Priyadarshini Thirunavukkarasu created a post,
Combine GVCFs
AnsweredI am using GATK 4.2.2.0-foss-2018b-Java-1.8 version to combine GVCF files. But, I get the below warning as invalid annotation at chromosome 2 and exception thrown at chromosome 5 09:07:30.141 INFO ...