BaseQualityCheck - Revision history

Zhanxw at 08:35, 27 August 2010

2010-08-27T08:35:50Z

← Older revision		Revision as of 04:35, 27 August 2010
Line 1:		Line 1:
	'''Base Quality Check'''		'''Base Quality Check'''

	'''(~~May 11~~, 2010 - Paul, Xiaowei)'''		'''(Aug 27, 2010 - Paul, Xiaowei)'''


Line 17:		Line 17:
	'''Syntax''':		'''Syntax''':

	baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R]		baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R] [-2]
	-c -> only process first (max record count) of alignment.		-c -> only process first (max record count) of alignment.
	-q -> alignment with less than minimum mapping quality will not be counted		-q -> alignment with less than minimum mapping quality will not be counted
Line 25:		Line 25:
	-g -> output in GNU Plot code, you can pipe the output using '\|gnuplot'		-g -> output in GNU Plot code, you can pipe the output using '\|gnuplot'
	-R -> output in R code, you can pipe the output using '\|Rscript --vanilla - '		-R -> output in R code, you can pipe the output using '\|Rscript --vanilla - '
			-2 -> use SNP position for color space reads

	Example:		Example:
	Check first 20000 lines of abc.sam, using /data/local/ref/karma.ref/human.g1k.v37.fa as reference genome, excluding SNP sites specified in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl		Check first 20000 lines of abc.sam, using /data/local/ref/karma.ref/human.g1k.v37.fa as reference genome, excluding SNP sites specified in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl

Zhanxw at 04:00, 13 May 2010

2010-05-13T04:00:46Z

← Older revision		Revision as of 00:00, 13 May 2010
Line 24:		Line 24:
	-v -> output SAM record in which mismatched bases exist		-v -> output SAM record in which mismatched bases exist
	-g -> output in GNU Plot code, you can pipe the output using '\|gnuplot'		-g -> output in GNU Plot code, you can pipe the output using '\|gnuplot'
	-r -> output in R code, you can pipe the output using '\|Rscript --vanilla - '		-R -> output in R code, you can pipe the output using '\|Rscript --vanilla - '

	Example:		Example:

Zhanxw at 04:00, 13 May 2010

2010-05-13T04:00:33Z

← Older revision		Revision as of 00:00, 13 May 2010
Line 17:		Line 17:
	'''Syntax''':		'''Syntax''':

	baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v]		baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R]
	-c -> only process first (max record count) of alignment.		-c -> only process first (max record count) of alignment.
	-q -> alignment with less than minimum mapping quality will not be counted		-q -> alignment with less than minimum mapping quality will not be counted
Line 23:		Line 23:
	-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl		-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
	-v -> output SAM record in which mismatched bases exist		-v -> output SAM record in which mismatched bases exist
			-g -> output in GNU Plot code, you can pipe the output using '\|gnuplot'
			-r -> output in R code, you can pipe the output using '\|Rscript --vanilla - '

	Example:		Example:

Zhanxw at 03:01, 12 May 2010

2010-05-12T03:01:24Z

← Older revision		Revision as of 23:01, 11 May 2010
Line 9:		Line 9:

	It read SAM/BAM file line by line. Then according to CIGAR string, it compares the alignment to reference genome (base by base) and record match and mismatch frequencies grouped by observed base quality.		It read SAM/BAM file line by line. Then according to CIGAR string, it compares the alignment to reference genome (base by base) and record match and mismatch frequencies grouped by observed base quality.
	The output will be observed quality (generated by Illumina machine) and empirical quality (calculated by Prob(Mismatch bases \| base quality Q) = (Total number of mismatched bases with base quality Q) / (Total number of bases with base quality Q)), both in Phred quality score.		The output will be observed quality (generated by Illumina machine) and empirical quality (calculated by Prob(Mismatch bases \| base quality Q) = (Total number of mismatched bases with base quality Q) / (Total number of bases with base quality Q)), both in Phred quality score. For convenience, you can pipe the output by '\| Rscript --vanilla -' to obtain a graph.

	By default, we omit soft clips, insertion and deletion.		By default, we omit soft clips, insertion and deletion.

Zhanxw at 02:59, 12 May 2010

2010-05-12T02:59:34Z

← Older revision		Revision as of 22:59, 11 May 2010
Line 18:		Line 18:

	baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v]		baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v]
	-c -> only process first (max record count).		-c -> only process first (max record count) of alignment.
	-q -> alignment with less than minimum mapping quality will not be counted		-q -> alignment with less than minimum mapping quality will not be counted
	-r -> reference genome (in KARMA format)		-r -> reference genome (in KARMA format)
Line 24:		Line 24:
	-v -> output SAM record in which mismatched bases exist		-v -> output SAM record in which mismatched bases exist

			Example:
			Check first 20000 lines of abc.sam, using /data/local/ref/karma.ref/human.g1k.v37.fa as reference genome, excluding SNP sites specified in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
			baseQualityCheck -c 20000 -r /data/local/ref/karma.ref/human.g1k.v37.fa -s /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl abc.sam


	Thank '''Bingshan''' for his qPlot program and his input to finish this program.		Thank '''Bingshan''' for his qPlot program and his input to finish this program.

Zhanxw at 02:50, 12 May 2010

2010-05-12T02:50:06Z

← Older revision		Revision as of 22:50, 11 May 2010
Line 8:		Line 8:
	'''Algorithm''':		'''Algorithm''':

	It read SAM/BAM file line by line~~; then~~ according to CIGAR string, it compares the alignment to reference genome base by base~~, then group~~ match and mismatch frequencies by observed base quality.		It read SAM/BAM file line by line. Then according to CIGAR string, it compares the alignment to reference genome (base by base) and record match and mismatch frequencies grouped by observed base quality.
	The output will be observed quality (generated by Illumina machine) and empirical quality (~~generated~~ by Prob(Mismatch bases \| base quality Q) = (Total number of mismatched bases\| base quality Q) / (Total number of bases\| base quality Q)).		The output will be observed quality (generated by Illumina machine) and empirical quality (calculated by Prob(Mismatch bases \| base quality Q) = (Total number of mismatched bases with base quality Q) / (Total number of bases with base quality Q)), both in Phred quality score.
	We omit soft clips, insertion and deletion.
			By default, we omit soft clips, insertion and deletion.

			Note, we strongly recommend excluding dbSNP sites, or else you are likely to underestimate empirical quality. The program can read a plain text file to specify dbSNP positions via '-s' option.

	'''Syntax''':		'''Syntax''':
Line 18:		Line 21:
	-q -> alignment with less than minimum mapping quality will not be counted		-q -> alignment with less than minimum mapping quality will not be counted
	-r -> reference genome (in KARMA format)		-r -> reference genome (in KARMA format)
	-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl		-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
	-v -> output SAM record in which mismatched bases exist		-v -> output SAM record in which mismatched bases exist

	Thank '''Bingshan''' for his qPlot program and his input to finish this program.		Thank '''Bingshan''' for his qPlot program and his input to finish this program.

Zhanxw at 02:42, 12 May 2010

2010-05-12T02:42:20Z

← Older revision		Revision as of 22:42, 11 May 2010
Line 1:		Line 1:
	'''Base Quality Check		'''Base Quality Check'''
	(May 11, 2010 - Paul, Xiaowei)'''
			'''(May 11, 2010 - Paul, Xiaowei)'''


	'''Location''': $(repository)/baseQualityCheck/baseQualityCheck		'''Location''': $(repository)/baseQualityCheck/baseQualityCheck

Zhanxw: Created page with ''''Base Quality Check (May 11, 2010 - Paul, Xiaowei)''' '''Location''': $(repository)/baseQualityCheck/baseQualityCheck '''Algorithm''': It read SAM/BAM file line by line; th…'

2010-05-12T02:40:52Z

Created page with ''''Base Quality Check (May 11, 2010 - Paul, Xiaowei)''' '''Location''': $(repository)/baseQualityCheck/baseQualityCheck '''Algorithm''': It read SAM/BAM file line by line; th…'

New page

'''Base Quality Check
(May 11, 2010 - Paul, Xiaowei)'''

'''Location''': $(repository)/baseQualityCheck/baseQualityCheck

'''Algorithm''':

It read SAM/BAM file line by line; then according to CIGAR string, it compares the alignment to reference genome base by base, then group match and mismatch frequencies by observed base quality.
The output will be observed quality (generated by Illumina machine) and empirical quality (generated by Prob(Mismatch bases | base quality Q) = (Total number of mismatched bases| base quality Q) / (Total number of bases| base quality Q)).
We omit soft clips, insertion and deletion.

'''Syntax''':

baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v]
-c -> only process first (max record count).
-q -> alignment with less than minimum mapping quality will not be counted
-r -> reference genome (in KARMA format)
-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
-v -> output SAM record in which mismatched bases exist

Thank '''Bingshan''' for his qPlot program and his input to finish this program.