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213 bytes added
, 04:35, 27 August 2010
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| '''Base Quality Check''' | | '''Base Quality Check''' |
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− | '''(May 11, 2010 - Paul, Xiaowei)''' | + | '''(Aug 27, 2010 - Paul, Xiaowei)''' |
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| '''Syntax''': | | '''Syntax''': |
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− | 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] [-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 |
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| -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 - ' |
| + | -2 -> use SNP position for color space reads |
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| 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 |