FreeBayes

[…] lasmids (pUSA01, pUSA02, and pUSA03). Duplicates were marked and excluded from further analysis using Picard2 RemoveDuplicates tool (http://broadinstitute.github.io/picard). SNPs were identified with Freebayes v1.0.2.29 [] using a list (-L) to compare all genomes from a single subject compared to the reference sequence (USA300_FPR3757) and filtered using SnpSift [] for the following qualities (MQM […]

[…] l samples’ Illumina reads where then mapped to this reference sequence using bwa version 0.7.5a []. After quality filtering and deduplication with samtools version 1.6 [], variants where called using freebayes version 1.1.0-50 [] and consensus sequences extracted as FASTA with bcftools version 1.6 []. The resulting sequences where aligned using Clustal Omega [], the alignment was checked and trimm […]

[…] apped to the National Veterinary Services Laboratory (NVSL) reference/challenge Cooper strain of BHV-1.1 (GenBank accession number JX898220) using the bwa-mem algorithm (). Variants were called using freebayes (). Low-quality variants were filtered out, and consensus sequences were obtained using the bcftools consensus tool (http://github.com/samtools/bcftools). Based on phylogenetic analysis, the […]

[…] eSeq datasets are downloaded in FASTQ format and aligned with BWA in Partek Flow. After that, duplicates are removed using Filter Alignments task and the variant calls are obtained using Samtools and Freebayes in Partek Flow. For WES data, the calls are restricted to the corresponding Nextera or TrueSeq target regions.All of the calls are restricted to chromosomes 1–22 and X (NA12878 is derived fr […]

[…] ntified.Maximum depth filter (DP): We removed the sites that were covered by excess number of reads as these sites are very likely to be located within a repeat or a multi-duplicated region. Although FreeBayes and SAMtools mpileup report the read depth in slightly different manner due to algorithm differences, we chose the same maximum depth value of 1,500, corresponding to a coverage of 24.6 read […]

[…] from GATK ‘best practices’ [] (see Additional file  for details). We used the resulting BAM format alignment data to call variants with: GATK HaplotypeCaller (3.3.0) [, ], SAMtools mpileup (1.3) [], FreeBayes (1.0.2) [], and Platypus (0.8.1) []. Each callset was normalized using vt normalize [] and the vcfallelicprimitives module in vcflib (https://github.com/ekg/vcflib) to deconstruct complex va […]