lmanchon

thx

yes, see attachment. [SAD190005_S6_gridss.vcf.txt](https://github.com/KarchinLab/open-cravat/files/10935519/SAD190005_S6_gridss.vcf.txt)

ACMG annotations are important, tools like Tapes (https://github.com/a-xavier/tapes) or AnnotSV (https://lbgi.fr/AnnotSV/) are able to provide this type of annotation. It would be valuable if Cravat was also able to render...

Hi, it seems in your complete table there are 2 columns (just after "baseMean" column) that represent the mean of normalised counts of each replicat. It's computed by this piece...

Yes, I understand. Thank you.

--Hi, same error on sam file: Program: samtools (Tools for alignments in the SAM format) Version: 1.3.1 (using htslib 1.3.1) samtools view -h -o D6_DMSO_sorted.sam D6_DMSO_sorted.bam BIOBAMBAM/bin/bamtofastq filename=D6_DMSO_sorted.sam inputformat=sam gz=1...

[sam_header.zip](https://github.com/gt1/biobambam2/files/1567485/sam_header.zip)

yes, but why others tools such as bedtools bam2fastq, bam2FastQ (BamUtil) or bam2fastq(https://github.com/jts/bam2fastq) are able to process this broken file ?

one way first is to remove bad Ct from technical replicates, to do this i use Dixon Q test to check which Ct is the best outlier

--Hi, i have read in some papers they use SEM instead of SD, this reduces the amplitude of the error bar. When s is the SD or SEM of the...