Compare GATK's internal pileup to a reference Samtools pileup
At every locus in the input set, compares the pileup data (reference base, aligned base from each overlapping read, and quality score) generated internally by GATK to a reference pileup data generated by Samtools. Note that the pileup program has been replaced in Samtools by mpileup, which produces a slightly different output format by default.
There are two versions of the original pileup format: the current 6-column format produced by Samtools, and the old 10-column "consensus" format which could be obtained by using the -c argument, now deprecated.
Each line consists of chromosome, 1-based coordinate, reference base, the number of reads covering the site, read bases and base qualities. At the read base column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch on the reverse strand. A pattern `\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence.
seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
seq1 273 T 23 ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+
seq1 274 T 23 ,.$....,,.,.,...,,,.,... 7<7;<;<<<<<<<<<=<;<;<<6
seq1 275 A 23 ,$....,,.,.,...,,,.,...^l. <+;9*<<<<<<<<<=<<:;<<<<
seq1 276 G 22 ...T,,.,.,...,,,.,.... 33;+<<7=7<<7<&<<1;<<6<
seq1 277 T 22 ....,,.,.,.C.,,,.,..G. +7<;<<<<<<<&<=<<:;<<&<
seq1 278 G 23 ....,,.,.,...,,,.,....^k. %38*<<;<7<<7<=<<<;<<<<<
seq1 279 C 23 A..T,,.,.,...,,,.,..... ;75&<<<<<<<<<=<<<9<<:<<
See the Pileup format documentation for more details.
The "consensus" or extended pileup consists of the following:
seq1 60 T T 66 0 99 13 ...........^~.^~. 9<<55<;<<<<<<
seq1 61 G G 72 0 99 15 .............^~.^y. (;975&;<<<<<<<<
seq1 62 T T 72 0 99 15 .$.............. <;;,55;<<<<<<<<
seq1 63 G G 72 0 99 15 .$.............^~. 4;2;<7:+<<<<<<<
seq1 64 G G 69 0 99 14 .............. 9+5<;;;<<<<<<<
seq1 65 A A 69 0 99 14 .$............. <5-2<;;<<<<<<;
seq1 66 C C 66 0 99 13 ............. &*<;;<<<<<<8<
seq1 67 C C 69 0 99 14 .............^~. ,75<.4<<<<<-<<
seq1 68 C C 69 0 99 14 .............. 576<;7<<<<<8<< *
Escherichia_coli_K12 3995037 * *\/* 430 0 37 144 * +A 143 1 0
Escherichia_coli_K12 3995279 * *\/* 202 0 36 68 * +A 67 1 0
Escherichia_coli_K12 3995281 * *\/* 239 0 36 67 * -CG 66 1 0
See Consensus pileup format (deprecated) for more details.
A BAM file containing your aligned sequence data and a pileup file generated by Samtools covering the region you want to examine.
A text file listing mismatches between the input pileup and the GATK's internal pileup. If there are no mismatches, the output file is empty.
java -jar GenomeAnalysisTK.jar \ -T CheckPileup \ -R reference.fasta \ -I your_data.bam \ --pileup:SAMPileup pileup_file.txt \ -L chr1:257-275 \ -o output_file_name
These Read Filters are automatically applied to the data by the Engine before processing by CheckPileup.
This tool can be run in multi-threaded mode using this option.
This tool applies the following downsampling settings by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --pileup |
NA | Pileup generated by Samtools | |
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Flags | |||
| --continue_after_error |
false | Continue after encountering an error | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Continue after encountering an error
By default the program will quit if it encounters an error (such as missing truth data for a given position).
Use this flag to override the default behavior; the program will then simply print an error message and move on
to the next position.
boolean false
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout
Pileup generated by Samtools
This is the existing pileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.
This argument supports reference-ordered data (ROD) files in the following formats: SAMPILEUP
R RodBinding[SAMPileupFeature] NA