Tag: mnp

A new study has found that, globally, micro- and nanoplastics and plastic additives are widespread across our food supply. While we have an understanding of how they get there, we don’t know a lot about their effects on human health, food safety and security. The average person discards about 77…

Using GATK Mutect2, we collected several variants in EGFR region. However, one variants NM_005228.5(EGFR):c.2239_2248delinsC (p.Leu747_Ala750delinsPro) were called as two separated ones. The two variants can not combined even we set the -max-mnp-distance to 20. 7 55242465 . GGAATTAAGA G . .AS_SB_TABLE=5567,5732|44,36;DP=11794;ECNT=2;MBQ=20,20;MFRL=188,168;MMQ=60,60;MPOS=39;NALOD=3.85;NLOD=1755.82;POPAF=4.52;TLOD=256.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB0|1:2957,80:0.027:3037:1304,28:1306,51:0|1:55242465_GGAATTAAGA_G:55242465:1402,1555,44,36 0|0:8342,0:1.710e-04:8342:3598,0:4195,0:0|1:55242465_GGAATTAAGA_G:55242465:4165,4177,0,0 7 55242478 . G C . .AS_SB_TABLE=5360,5529|44,36;DP=11030;ECNT=2;MBQ=20,20;MFRL=189,168;MMQ=60,60;MPOS=43;NALOD=3.93;NLOD=1686.18;POPAF=4.52;TLOD=256.12…

Deoxynivalenol (DON) is one of the subgroup B mycotoxins, mainly produced by Fusarium species, and reported to be the predominant contaminant in the environment and food [17], [26]. The toxic effects of DON include immune modulation, disruption of intestinal barrier function, and cytotoxicity leading to cell death [13], [8]. Due…

RDS file in Rstudio 0 Hello, I have downloaded the RDS file here, the “MNP-VERSE”. I am trying to extract all the cells and their value for a specific tissue in a specific gene (e.g. breast tissue and MSR1 gene). So far I get this: library(tidyverse) filename <- file.choose() msr1…

I have a treatment vcf file and three control vcf files. This has been generated from somatic variants on RNAseq data. I want to extract variants that are in treatment sample but not in control groups. To do so, I first normalized them using bcftools norm -m -any command, then…

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…