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comparison pileup_parser.xml @ 1:d31417e25765 draft

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author devteam
date Tue, 03 Jun 2014 12:39:46 -0400
parents 5c3984014c07
children ffeb59f7a82d
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0:5c3984014c07 1:d31417e25765
318 chrM 414 C 4 ..Ta III2 318 chrM 414 C 4 ..Ta III2
319 chrM 415 C 4 TTTt III7 319 chrM 415 C 4 TTTt III7
320 320
321 To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows: 321 To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:
322 322
323 .. image:: ${static_path}/images/pileup_parser_help1.png 323 .. image:: pileup_parser_help1.png
324 324
325 Running the tool with these parameters will return:: 325 Running the tool with these parameters will return::
326 326
327 chrM 413 G 4 ..t, IIIH 0 0 0 1 3 327 chrM 413 G 4 ..t, IIIH 0 0 0 1 3
328 chrM 414 C 4 ..Ta III2 0 2 0 1 3 328 chrM 414 C 4 ..Ta III2 0 2 0 1 3
334 334
335 **Example 2**: Report everything 335 **Example 2**: Report everything
336 336
337 In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters: 337 In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:
338 338
339 .. image:: ${static_path}/images/pileup_parser_help2.png 339 .. image:: pileup_parser_help2.png
340 340
341 will report everything from the original file:: 341 will report everything from the original file::
342 342
343 chrM 412 A 2 ., II 2 0 0 0 2 343 chrM 412 A 2 ., II 2 0 0 0 2
344 chrM 413 G 4 ..t, III2 0 0 2 1 3 344 chrM 413 G 4 ..t, III2 0 0 2 1 3
353 353
354 **Example 3**: Report everything and print total number of differences 354 **Example 3**: Report everything and print total number of differences
355 355
356 If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this: 356 If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:
357 357
358 .. image:: ${static_path}/images/pileup_parser_help3.png 358 .. image:: pileup_parser_help3.png
359 359
360 will produce this:: 360 will produce this::
361 361
362 chrM 412 A 2 ., II 2 0 0 0 2 0 362 chrM 412 A 2 ., II 2 0 0 0 2 0
363 chrM 413 G 4 ..t, III2 0 0 2 1 3 1 363 chrM 413 G 4 ..t, III2 0 0 2 1 3 1
369 369
370 **Example 4**: Report everything, print total number of differences, and ignore qualities and read bases 370 **Example 4**: Report everything, print total number of differences, and ignore qualities and read bases
371 371
372 Setting **Print quality and base string?** to **Yes** as shown here: 372 Setting **Print quality and base string?** to **Yes** as shown here:
373 373
374 .. image:: ${static_path}/images/pileup_parser_help4.png 374 .. image:: pileup_parser_help4.png
375 375
376 will produce this:: 376 will produce this::
377 377
378 chrM 412 A 2 2 0 0 0 2 0 378 chrM 412 A 2 2 0 0 0 2 0
379 chrM 413 G 4 0 0 2 1 3 1 379 chrM 413 G 4 0 0 2 1 3 1