More posts like this
-
Non variants sites of the genome (gVCF file)
written by heureuse 1Hello, I have 10000 individuals and I would like to create a file where I put all the non variants sites and their coverage. The …
-
CNV detection
written by heureuse 1Hello all, I saw a post about detecting CNV from VCF file. People advised to avoid doing that and use a bam file instead. My …
-
NA12878, NA12891 and NA12892 gold standard samples information
written by heureuse 1Hello, I'm building a pipeline For CNV calling and I would like to validate using this trios NA12878, NA12891 and NA12892. I don't know where …
-
Mendelian precison
written by heureuse 1Hello, I would like to validate CNV using trios (father, mother and offspring) using mendelian precision. I'm not able to find a paper talking about …
-
golden genome NA12878
written by heureuse 1Hello, Do you know where I can find sample WGS of NA12878 and how I can convert it in gVCF format ? thank you
-
How to slice a CRAM file into the 50kb regions padded with 1kb?
written by Sd 0Hello, I am working on whole genome sequencing CRAM files and I want to perform GATK best practice. Before that, I want to slice each …
-
Converting multiple cram files to fastq files.
written by Rose 0Hello everyone, I need help with converting cram files to fastq files. I have many cram files with me and want to convert them to …
-
Variant splicing position on CDS
written by heureuse 1Hello, I would like to know how I can find the position of a variant splicing on coding sequence. I'm using Aloft but if there …
-
how to convert ped files to cnv
written by iag.14800108 0Hello, I am new to bioinformatics. I would like to know how I can convert my ped and map files to cnv? so I can …
-
How to filter VCF with HRun > 8 and AB > 0.2 and AB < 0.2
written by pegeot.henri 0Hello, I have vcf files containing R8 and LowVariantFreq variants (they are flagged as PASS) and I would like to filter out these variants. I …