Pileup - Revision history

Mktrost at 19:06, 3 April 2012

2012-04-03T19:06:15Z

← Older revision		Revision as of 15:06, 3 April 2012
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	[[Category:StatGen Download]]		[[Category:StatGen Download]]
	[[Category:BAM Software]]		[[Category:BAM Software]]

			This program will be re-released soon (April, 2012).

	Features:		Features:

Mktrost at 20:33, 19 January 2011

2011-01-19T20:33:31Z

← Older revision		Revision as of 16:33, 19 January 2011
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			[[Category:Software]]
			[[Category:StatGen Download]]
			[[Category:BAM Software]]

	Features:		Features:
	# Option to include a VCF file to select chromosome locations of interest		# Option to include a VCF file to select chromosome locations of interest

Mktrost at 20:32, 19 January 2011

2011-01-19T20:32:26Z

← Older revision		Revision as of 16:32, 19 January 2011
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	Features:		Features:
	# Option to include a VCF file to select chromosome locations of interest		# Option to include a VCF file to select chromosome locations of interest
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	== HELP SCREEN ==		== HELP SCREEN ==
	<pre>		<pre>
	./~~gpileup~~ -h		./mgpileup -h


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	./~~gpileup~~ [-v <string>] [-i <string>] -r <string> -b <string> [-d] [--]		./mgpileup [-v <string>] [-i <string>] -r <string> -b <string> [-d] [--]
	[--version] [-h]		[--version] [-h]

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	./~~gpileup~~ -r /data/local/ref/karma.ref/human.g1k.v37 -b		./mgpileup -r /data/local/ref/karma.ref/human.g1k.v37 -b
	../data/HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.bam -v		../data/HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.bam -v
	HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.vcf -i -i		HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.vcf -i -i

Mktrost: Created page with ' Features: # Option to include a VCF file to select chromosome locations of interest #* Input VCF file can be gzipped or plain text. #*The output VCF file when an input VCF file …'

2010-11-01T21:34:10Z

Created page with ' Features: # Option to include a VCF file to select chromosome locations of interest #* Input VCF file can be gzipped or plain text. #*The output VCF file when an input VCF file …'

New page

Features:
# Option to include a VCF file to select chromosome locations of interest
#* Input VCF file can be gzipped or plain text.
#*The output VCF file when an input VCF file is specified will contain a subset of locations found in the input VCF file
# Reads BAM index file to have direct access to chromosome locations of interest
#* BAM index file is assumed to be in the same directory as the bam file with the additional extension .bai
# The user is responsible for ensuring that the chromosome name in the input VCF file and the BAM file are consistent with one another.

== HELP SCREEN ==
<pre>
./gpileup -h

USAGE:

./gpileup [-v <string>] [-i <string>] -r <string> -b <string> [-d] [--]
[--version] [-h]

Where:

-v <string>, --ouputvcf <string>
VCF file - if the extension is .gz, the written file will be a gzip
file, (default is STDOUT)

-i <string>, --inputvcf <string>
VCF file listing the loci of interest (can be gzipped), bam index file
is automatically assumed to be in the same location as the bam file.

-r <string>, --reference <string>
(required) Reference Sequence file

-b <string>, --bam <string>
(required) BAM file

-d, --adddelasbase
Adds deletions as base

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

Example:

./gpileup -r /data/local/ref/karma.ref/human.g1k.v37 -b
../data/HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.bam -v
HG00160.chrom20.ILLUMINA.bwa.GBR.low_coverage.20100517.vcf -i -i
../data/LDL_b37.modified.genos.EUR.vcf -d

Pileup takes in a BAM file and a genome reference file to return the
following

Alignment statistics are written to the VCF file specified, if the file
name ends with .gz, the file output will be in gzip format.

1. CHROM : chromosome.

2. POS : position on chromosome.

3. ID : id.

4. REF : Reference base in the reference genome. A,C,T,G,N.

5. ALT : alt.

6. QUAL : quality score.

7. FILTER : filter.

8. INFO : info.

9. FORMAT : headers of custom data.

a. N : number of contigs mapped at this locus.

b. BASE : bases of respective contigs, '-' for deletions.

c. MAPQ : quality score of the mapping for the contig, this is also
shown for deletions.

d. BASEQ : phred quality score, -1 for deletions.

e. STRAND : F - forward, R - reverse.

f. CYCLE : sequencing cycle, -1 for deletions.

g. GL : genotype likelihood scores - AA,AC,AG,AT,CC,CG,CT,GG,GT
,TT.

10. <vcf output file name> : contains data described in FORMAT.
</pre>