I run the tool from inside IVG and it gives the error: "Your input file has a malformed header:The FORMAT field was provided but there is on genotype/sample data"
Do you know how to fix this?
-
You can generate the index using igvtools, either from the command line or from the IGV gui.
Actually, the command line version never works for me. It gives the error, "Exception in thread "main" org.broad.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw a header line specifying VCF version". But running the tool from inside IGV has no problem.Leave a comment:
-
Create vcf tribble index?
Hi, I'm using the GaTK to call variants, and afterward I somehow managed to delete some of the .vcf.idx index files. Without those files the GaTK can't read the vcf files. Is there a way to (re-) build the .idx indexes without re-running the UnifiedGenotyper? Couldn't find one in the GaTK documentation. (I read about tabix, but he requires bgzipped input, which I'm not sure the GaTK can handle)
Thanks!
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...09-26-2023, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM
Leave a comment: