Jaime Alvarez Benayas
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Activity overview
Latest activity by Jaime Alvarez Benayas-
Jaime Alvarez Benayas commented,
Thank you very much for the help Gökalp Çelik
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Jaime Alvarez Benayas commented,
Thank you Gökalp Çelik it does help a lot. What about the opposite case? Variants filtered as "germline" but not found in the germline population frequency resource. I am assuming this is because t...
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Jaime Alvarez Benayas created a post,
Mutect2 calls germline variants not present in germline resource
a) GATK version used: 4.5.0.0 I am seeing differences between two tumor states b) Exact command used: Mutect2 -R /data/genome/hg38ucsc/hg38_no_alt.fa -I Tumor2.bam -I Tum...
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Jaime Alvarez Benayas commented,
Hi Thomas Bradley, I am doing a similar kind of analysis as what you described (pseudonormal = tumor state 1, tumor = tumor state 2). Did you manage to run successfully the analysis you were descri...
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Jaime Alvarez Benayas created a post,
Somatic variants lost when --genotype-germline-sites true
REQUIRED for all errors and issues: a) GATK version used: 4.5.0.0b) Exact command used: I am calculating the exact same variants, in one case with default value for --genotype-germline-sitesMutect...
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Jaime Alvarez Benayas created a post,
Calculating variations between two tumor states
Hello: Given that I have two related tumor samples at different timepoints, I want to see changes between both. I have used mutect2 with one of the samples as "tumor" and the other as "normal", I h...
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Jaime Alvarez Benayas commented,
Thank you, it did help!
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Jaime Alvarez Benayas created a post,
Mutect2 using a tumor as "pseudonormal" and relapsed as "tumor", PON necessary?
Hello: I have seen that it is possible to use Mutect2 using a tumor as "pseudonormal" and relapsed as "tumor" (#6 on this page: https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-fo...
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Jaime Alvarez Benayas created a post,
Germline pipeline - incorrect read depth reported after filtering variants.
After filtering variants, the read depth is incorrect: a) GATK version used: 4.5.0.0b) Exact command used: HaplotypeCaller on one sample (C419T_Matrigel) export OMP_NUM_THREADS=4; gatk --java-...
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Jaime Alvarez Benayas created a post,
Funcotator gnomAD incoherent number of output fields
a) GATK version used: 4.5.0.0 Funcotator germline with gnomAD is producing incoherent number of output fields. I am showing an example for a variant at chr1 598934 GATK version used: 4.5.0.0 I h...