Sentence examples for sources of variant from inspiring English sources

Other efforts have been made to understand the sources of variant calling errors [ 12].

Both pipelines include a filtering step (mdust filtering) that removes variants falling into LCRs, as recommended by a recent study on the sources of variant calling errors (Li 2014).

One can identify and set aside reads that map to multiple locations in the genome with nearly equal alignment quality, denoting such cases as potential sources of variant-calling errors.

Two different sources of variants were used: (1) single nucleotide variants (SNV) and structural variants (SV) from genome sequencing (2.1) and (2) SNVs and SVs called in an initial alignment round of the RNA-Seq reads to the TAIR10 reference genome with PALMapper (relevant parameters: -M 4 -G 4 -E 6 -I 25000 -NI 1 -S).

For both sources of variants we applied stringent filter criteria to reduce false calls: (1) genome variants had to appear in at least 40 strains with a minor allele count of at least 5 strains, (2) RNA-Seq variants had to be confirmed by at least 2 alignments within the same strain and had to have less than factor 2 many non-confirming alignments within the same strain.

The rationale for this intervention is that it removes the main source of variant TTR (vTTR).

These will be a major source of variants that characterize the population.

Association panels or population samples can also provide a reliable source of variants given a sufficiently large sample size and minor allele frequency.

Our analysis of the high-throughput articles also led to consideration of another important source of variants, information external to, but associated with, the main article, such as supplementary material.

In cases in which the analysis target is the only source of variants, we and other GATK users have had some success by taking the analysis target through the naive pipeline, hard filtering to generate a temporary sensitive variant resource, and using that temporary sensitive variant resource to BQSR the analysis target.

However, due to technical sources of noise, variant alleles in both tumour and normal samples can be observed at frequencies that are less than expected and can be difficult to detect.