Jenifer
- Total activity 35
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 1
- Subscriptions 13
Activity overview
Latest activity by Jenifer-
Jenifer commented,
Okay thanks! Both cohorts are solid tumour samples, but I don't know their purity. I just wanted to be sure that this can be normal and not caused by mutect2 avoiding to call variants with high VAFs.
-
Jenifer created a post,
VAF distribution of Mutect2 tumour-normal matched calling
Hi!I have performed some mutect2 (v 4.1.7.0) variant callings using the following command line: gatk Mutect2 -R "$reference" \--tumor-sample $tumour1ID --normal-sample $normalID --input $tumour1Bam...
-
Jenifer commented,
Genevieve Brandt (she/her) Thanks for the clarification, I understand. I'll remove this kind of variants then.
-
Jenifer commented,
This is the log (I'm not showing most progressMeter lines): jdk/8u181 loaded gatk/4.1.7.0 loaded Using GATK jar /mnt/gatk/4.1.7.0/gatk-package-4.1.7.0-local.jar Running: java -Dsamjdk.use_async_i...
-
Jenifer commented,
It is gatk version 4.1.7.0
-
Jenifer commented,
Sure Genevieve Brandt (she/her): This is an example: First two genotype fields refer to two different tumour samples and the third refers to the matched-normal. As you can see, there are six reads ...
-
Jenifer commented,
Hi Genevieve Brandt (she/her)!I've read the troubleshooting but I haven't found an answer to my question. I thought Mutect2 was designed to call just somatic calls and, therefore, not to call those...
-
Jenifer created a post,
Why do I see a variant called by mutect2 in my matched-normal sample when checking the results?
AnsweredHi!I am trying to find subclonal variants in a sample sequenced with high coverage (a ~1000x gene panel). After using mutect2 to call SNVs and INDELs in normal-matched mode, I've detected that some...
-
Jenifer commented,
Hi!This is also happening to me. My problem is that I am working in a cluster so I cannot write at gatk directory. Do you know if I can solve this without modifying the Rscript? I am using gatk/4.1...
-
Jenifer created a post,
Is it okay to run multiple instances of BQSR with the -L argument in order to increase the speed of the workflow?
AnsweredHi!I would like to run in parallel multiple instances of a BQSR workflow in order to increase its speed. As I achieve this, for example, for mutect2 pipeline by specifying the -L argument to each c...