What does SAMtools mpileup do?

What does SAMtools mpileup do?

The SAMtools mpileup utility provides a summary of the coverage of mapped reads on a reference sequence at a single base pair resolution. In addition, the output from mpileup can be piped to BCFtools to call genomic variants.

How does BCFtools Mpileup work?

The principal feature to SAMtools mpileup is the ability to analyze data from multiple samples simultaneously. This is useful for detecting variants in low-coverage regions by leveraging data across samples. You can also use the bcftools pipeline for multi-sample calling.

What is a pileup file?

Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment.

Is Bcftools part of samtools?

See bcftools call for variant calling from the output of the samtools mpileup command. In versions of samtools <= 0.1. Users are now required to choose between the old samtools calling model (-c/–consensus-caller) and the new multiallelic calling model (-m/–multiallelic-caller).

What does a VCF file look like?

VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. The format also has the ability to contain genotype information on samples for each position.

How do I view a BCF file?

To view a BCF file:

1. Open the Vectorworks file that is associated with the BCF file.
2. Select AEC > Open BCF Viewer.
3. If no BCF file is currently imported into this Vectorworks file, the Import BCF dialog box opens.
4. The BCF Viewer dialog box opens and displays data from the imported file.

What is the new mapping quality for mpileup?

Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt ( (INT-q)/INT)*INT.

Are there any evaluations of indel calling tools?

Despite many indel calling tools, evaluation of the tools objectively, particularly using large-scale real data, is sparse. There is an evaluation of four indel (Dindel, VarScan, GATK Unified Genotyper, and SAMtools) tools done by Neuman et al.; however, it was based on simulated data [ 39 ].

Which is the best parameter to apply to mpileup?

One should consider to apply the following parameters to mpileup in different scenarios: Apply -C50 to reduce the effect of reads with excessive mismatches. This aims to fix overestimated mapping quality and appears to be preferred for BWA-short.

How are field and tag names displayed in mpileup?

In the mpileup output, tag columns are displayed in the order they were provided by the user in the command line. Field and tag names have to be provided in a comma-separated string to the mpileup command. E.g.