M Carta
- Total activity 11
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 2
- Subscriptions 4
Activity overview
Latest activity by M Carta-
M Carta commented,
Thank you Gökalp Çelik. I tried adding the option suggested by you, but I'm afraid that the output VCF is still empty: gatk Mutect2 \-R "hg38.fa" \--alleles "variant.vcf.gz" \--genotype-germline-si...
-
M Carta created a post,
Mutect2 forced calling via --alleles does not always generate an output
I am attempting to force Mutect2 to call a particular variant of interest, given in variant.vcf.gz, using the following command: gatk Mutect2 \-R "hg38.fa" \--alleles "variant.vcf.gz" \-L "variant....
-
M Carta created a post,
Does IGV perform filtering when displaying reads?
I have noticed that the read counts displayed in IGV are slightly lower than those in the AD field in the respective VCF files. Is it possible that IGV does not display certain reads (perhaps poor ...
-
M Carta created a post,
Is there a GATK tool for quantifying a particular base?
Apologies if this is a naive question, but I'm quite new to bioinformatics.I'm working with targeted Illumina sequencing data generated with DNA from diseased and healthy tissue (this is an age-rel...
-
M Carta created a post,
Mutect2 Unable to trim uncertain bases without flow order information
Hi everyone. I'm trying to run Mutect2 on some Illumina sequencing files that were processed as follows (GATK best practices): trimmed with Trimmomatic, mapping with Minimal2, converted to BAM with...