Furthermore, the biases resulting from the conventional estimator and its variant for the non-normal sample are larger relative to the normal sample indicating that the estimator is sensitive to the normality assumption.
This was not surprising as the normal sample, acquired one month after diagnosis, was known to contain 10 15% blasts.
To estimate allelic copy number, germline heterozygous sites in the normal sample were called via GATK Haplotype Caller21,27.
The authors sent it to a leading American forensics laboratory, which analyzed it as if it were a normal sample of a man's blood.
The authors sent it to a leading American forensics laboratory, which analysed it as if it were a normal sample of a man's blood".
To account for tumor-in-normal contamination (e.g. case SJHGG003_A), we required tumor MAF > 0.05 if mutant reads were observed in the normal sample for "Somatic" calls.
For each tumor or normal sample, Picard checks for contamination, aligns reads to hg19, and calculates quality metrics, resulting in a single de-multiplexed, aggregated BAM file (see http://samtools.github.io/hts-specs/SAMv1.pdf).
The survey is ICM's preliminary prediction poll, with a larger than normal sample size, and will be updated on polling day after additional interviews being conducted into Wednesday night are fed into the data.
The initial gel viscosity was slightly higher, and the ultimate viscosity was 15%% lower than that of normal sample.
No matched normal sample was available for the 13 established cell lines included in the study.
We present readDepth, a new R package for CNA detection that does not require the sequencing of matched normal sample.
