This app applies samtools mpileup and creates an mpileup based on the provided BAM and BED. It can also optionally produce some summary statistics if required.
The mpileup file lists the bases observed at each position that meet the criteria provided.
This app requires the following data:
- skip - default True. the app will only run if skip is set to false.
- Compressed reference genome including
*.faand*.fa.fai(*.tar.gz) - BAM file(s) (
*.bam). If multiple BAM files are given a seperate analysis will be performed on each BAM file. - BED file of regions of interest, for filtering output vcf (
*.bed) - mpileup_summary_calcs (boolean) - default true. Set to false if summary statistics not required
The following samtools mpileup can be specified. if not given the app defaults are applied (stated in square brackets):
- min-MQ: Minimum mapping quality for an alignment to be used (-q) [20]
- extra arguments (string)
- min-BQ: Minimum base quality for a base to be considered (-Q) [10]
This app uses samtools 1.10-3
samtools mpileupcreates an mpileup file.
This app will output:
- samtools mpileup file, output to
/coverage/mpileup. This lists the base calls made at each position in the BED that meet the given criteria. For further information on the mpileup format please see the Documentation - optionally a summary calculations file containing:
- chromosome, pos, ref base and coverage depth at that position
- count of the reference base (refered to in the mpileup file as . or ,)
- counts of each A/C/T/G base NOTE: this will count every occurence of a or A (etc) in the line, which may include inserted or deleted bases this means that around homopolymer tracks there may be a higher number of e.g. A's than the total depth at that position.
- count of every insertion or deletion that begins at this position (+ or -)
- count of all deleted bases at that position (*)
- count of the final bases in the read (^)
This applet was developed by Synnovis Genome Informatics