Category
Generic
Usage
validateFiles -chromInfo=FILE -options -type=FILE_TYPE file1 [file2 [...]]
Manual
This tool is part of UCSC Genome Browser's utilities.
-type=
fasta : Fasta files (only one line of sequence, and no quality scores)
fastq : Fasta with quality scores (see http://maq.sourceforge.net/fastq.shtml)
csfasta: Colorspace fasta (implies -colorSpace)
csqual : Colorspace quality (see link below)
See http://marketing.appliedbiosystems.com/mk/submit/SOLID_KNOWLEDGE_RD?_JS=T&rd=dm
bam : Binary Alignment/Map
See http://samtools.sourceforge.net/SAM1.pdf
bigWig : Big Wig
See http://genome.ucsc.edu/goldenPath/help/bigWig.html
bedN[+P] : BED N or BED N+ or BED N+P
where N is a number between 3 and 15 of standard BED columns,
optional + indicates the presence of additional columns
and P is the number of addtional columns
Examples: -type=bed6 or -type=bed6+ or -type=bed6+3
See http://genome.ucsc.edu/FAQ/FAQformat.html#format1
bigBedN[+P] : bigBED N or bigBED N+ or bigBED N+P, similar to BED
See http://genome.ucsc.edu/goldenPath/help/bigBed.html
tagAlign : Alignment files, replaced with BAM
pairedTagAlign
broadPeak : ENCODE Peak formats
narrowPeak These are specialized bedN+P formats.
gappedPeak See http://genomewiki.cse.ucsc.edu/EncodeDCC/index.php/File_Formats
bedGraph : BED Graph
rcc: NanoString RCC
idat : Illumina IDAT
-as=fields.as If you have extra "bedPlus" fields, it's great to put a definition
of each field in a row in AutoSql format here. Applies to bed-related types.
-tab If set, expect fields to be tab separated, normally
expects white space separator. Applies to bed-related types.
-chromDb=dbSpecify DB containing chromInfo table to validate chrom names
and sizes
-chromInfo=file.txt Specify chromInfo file to validate chrom names and sizes
-colorSpaceSequences include colorspace values [0-3] (can be used
with formats such as tagAlign and pairedTagAlign)
-isSorted Input is sorted by chrom, only affects types tagAlign and pairedTagAlign
-doReport Output report in filename.report
-versionPrint version
For Alignment validations
-genome=path/to/hg18.2bit REQUIRED to validate sequence mappings match the genome specified
in the .2bit file. (BAM, tagAlign, pairedTagAlign)
-nMatch N's do not count as a mismatch
-matchFirst=n Only check the first N bases of the sequence
-mismatches=n Maximum number of mismatches in sequence (or read pair)
-mismatchTotalQuality=nMaximum total quality score at mismatching positions
-mmPerPair Check either pair dont exceed mismatch count if validating
pairedTagAlign files (default is the total for the pair)
-mmCheckOneInN=n Check mismatches in only one in 'n' lines (default=1, all)
-allowOtherAllow chromosomes that aren't native in BAM's
-allowBadLength Allow chromosomes that have the wrong length in BAM
-complementMinus Complement the query sequence on the minus strand (for testing BAM)
-bamPercent=N.N Percentage of BAM alignments that must be compliant
-privateData Private data so empty sequence is tolerated
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