Sentence examples for using the mpileup function from inspiring English sources

We initially called the SNPs using the mpileup function of SAMtools [ 45] with default parameters.

We call variants using the mpileup function in the Samtools package [ Li et al., 2009 ].

SNPs and indels were then called using the mpileup function in samtools, requiring a minimum base quality of 30.

Variant calling was conducted, using the mpileup function with default settings together with the current maize sequence (ZmB73_RefGen_v2) as reference.

Finally, single nucleotide polymorphisms were detected using the mpileup function in SAMtools [ 75] on the short read alignment file against P. abies created with BWA.

For transcriptome analyses, the base coverage at each nucleotide position was calculated using the mpileup function in Samtools (ver. 0.1.18 ) [ 50].

Variant calling was conducted using the mpileup function in SAMTools v1.18 [ 76] and the BCFTools package was used to filter SNPs with a minimum phred quality of 20 and a maximum read depth of 100.

The sorted BAM files were further processed in the variant calling step: using the "mpileup" function in SAMTools, indexed reference sequences and position sorted bam alignment files generated files with read information at sites where mismatches and indels from the reference sequence were detected.