From 27a8cedd8ef3199ed19ddb96ede9e2ff22166cac Mon Sep 17 00:00:00 2001 From: ljohansson Date: Mon, 24 Apr 2017 09:07:01 +0200 Subject: [PATCH] updated documentation --- .DS_Store | Bin 0 -> 12292 bytes docs/.DS_Store | Bin 0 -> 6148 bytes docs/README.md | 43 ++++++++++++++++++++++++++++++------------- docs/SUMMARY.md | 2 +- 4 files changed, 31 insertions(+), 14 deletions(-) create mode 100644 .DS_Store create mode 100644 docs/.DS_Store diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..4e980c2da67a473c3bffe85a9d3df787b0399eda GIT binary patch literal 12292 zcmeHMO>7%Q6n@W1+ub#7#`z;@QENy^gPK5`G);-1ah#;Iq@@8Tb<(DFZST^oy4elh zwOty5d~8dL-~b2^LgD~w3S3YRTtL8u3n0-R+6xj0xNzfy1W3Hu*@XOZ1eDH5GjHCT z_jdMu`|XZr3;>uY=rMo>08prM$->mEQusKpD@rJ^RFXuBhiu86&RR~E^zT-9OM^r} zA|Mfv2uK7Z0{;gDXwBwDS!3N7qq3CYLU{F+5QPZq(W@b+;)*6lN?U-$i&cr(Qb+tyjW1X|J5&Te98h3T}4rQI^E?m6y z!sRPh-xrBu@Uei%vcx}FoVDc^hsCKy$XO-p@LdCS+JP}M=h#W}ypd*AE~R{k)Zx5Q z^wW#vGFGl&Wjv$Lvbd9*$~jhH%67**HUXbe!4n`YJg zN=K(X)3M!SM&2da6mJ)|ttxYy>$mOL`M`sn`yRcyrHVzg8m%r>G+i@m8KWf**?7jy z8MbcPXO0t)wr4(V8hJH>U#TN@X37vz4dJaSyRJ;=H0KdV=RUeW5^e}@SCkXn-k&$9 z6=v<;aFfb1%7{xDh)XnUEh=->k+bydMCfjE!==x@ICwhKf+J&EBp?B zz@MmMHP&Dq*5fwZiTC3!Y{53%i{1Dz_Fx-aWa#W}o&*YOklRNPi*o`#PJeZIxdsJHO)5e_EDmpan9!v+jP_SCXR9f zF-54&;TDBB&O*Mb?GCqb2D1t=>N8VU*#f!`2`URBtLJ1~k(M6YIi2-~p(JFyG*V=wk$ z0tbj(Pv9^!-+U-8u2-ot1Ie3A zW+vGOn`8i_(Q-Nj1_1hOf=QGP5p(C%nmY?7&2fe?cJYkq>!KskDw<^P8#w2_4^iRE z{_jqg^cM(RxIj;EL7?C)AE{jW-O*#R1zsJ$_nc z;;U?R&9FS^^Mz zG^}AB}TGv+Ozu=$HvgYk#uF|@s&S{m!zxHp4Au(1Pwv{xcEctjevK#;>a9lr i2Xc;V>!i(R(dkzl8$-z=b`2-SLqG|ME*SU)2HpWLPbhc* literal 0 HcmV?d00001 diff --git a/docs/README.md b/docs/README.md index 083ca39..2a7defd 100644 --- a/docs/README.md +++ b/docs/README.md @@ -69,7 +69,7 @@ If no options are used the help menu will appear. [-inputDir, -outputDir, -bed, -controlsDir] OPTIONAL: [-rmDup, -useSampleAsControl] - StartWithAvgCount : + StartWithAvgCount : Start with Average Count files as input. This is a five column text file with predefined column names. Please read the manual for instructions. REQUIRED: @@ -110,7 +110,7 @@ If no options are used the help menu will appear. -controlSamples Number of samples to use in Match score analysis. DEFAULT: 30 -regionThreshold Percentage of all control samples differing more than 3 standard deviations from mean coverage of a region in the specified - BED file to exlude from sample ratio calculation. DEFAULT: 20 + BED file to exlude from sample CV calculation. DEFAULT: 20 -rmDup Switch to enable duplicate removal when using BAM files as input. -sexChr Switch to include sex chromosomes in analysis. -useSampleAsControl Switch to use samples as control. Example: when using BAM @@ -124,8 +124,8 @@ If no options are used the help menu will appear. this threshold are marked as deletion. DEFAULT: -3 -zScoreCutOffHigh Higher Z-score cutoff value. Regions with a Z-score above this threshold are marked as duplication. DEFAULT: 3 - -sampleRatioScore Sample ratio z-score cutoff value. Sample with a ratio - score below this value are excluded from analysis. DEFAULT: 0.09 + -sampleRatioScore Sample CV z-score cutoff value. Sample with a ratio + score below this value are excluded from analysis. DEFAULT: 0.09. NOTE: this variable now is named "SAMPLE CV" in all outputs! -percentageLessReliableTargets Target labelled as less reliable in percentage of control samples. DEFAULT: 20 ``` @@ -334,10 +334,11 @@ To apply a threshold of ratio score below 0.65 for a deletion and above 1.4 for The same thresholds for calling a deletion or duplication can also be applied using the Z-score value cutoff. To call a deletion when the Z-score is below -3 or duplication when the Z-score is above 3 use: ```bash - -zScoreCutOffLow -3 + -zScoreCutOffLow=-3 -zScoreCutOffHigh 3 ``` +Note that to use the minus variable in the -zScoreCutOffLow an '=' sign is needed instead of a space. To finetune the variant list one can generate a list of targets which in general are of lower quality in all possible controlsamples and apply this as a filter to generate a final list of high quality calls. This can be done by executing two steps: @@ -375,7 +376,6 @@ This produces the following output file: *.finallist.txt* contains all final calls, basically a filtered shortlist file. - # Test dataset A test dataset can be downloaded from [here](https://github.com/molgenis/CoNVaDING/tree/master/Test_dataset). @@ -501,15 +501,15 @@ The totallist contains the information of all targets and shows the ratio's and *Sample1.average.counts.best.score.totallist.txt* ```bash CHR START STOP GENE .. .. AUTO_VC .. .. .. ABBERATION QUALITY - 1 156104958 156105124 LMNA .. .. 0.06058213 .. .. .. DEL . + 1 156104958 156105124 LMNA .. .. 0.06058213 .. .. .. DEL . .. - 2 179511192 179511307 TTN .. .. 0.095184824 .. .. .. DEL . + 2 179511192 179511307 TTN .. .. 0.095184824 .. .. .. DEL . .. 6 7576507 7576710 DSP .. .. 0.051947043 .. .. .. DUP . - 6 7577172 7577296 DSP .. .. 0.094469481 .. .. .. DUP . - 6 7577992 7578140 DSP .. .. 0.061275822 .. .. .. DUP . + 6 7577172 7577296 DSP .. .. 0.094469481 .. .. .. DUP . + 6 7577992 7578140 DSP .. .. 0.061275822 .. .. .. DUP . .. - 12 21997397 21997507 ABCC9 .. .. 0.120684521 .. .. .. DUP LOW_QUALITY + 12 21997397 21997507 ABCC9 .. .. 0.120684521 .. .. .. DUP LOW_QUALITY .. 18 28647961 28648199 DSC2 .. .. 0.063042636 .. .. .. DEL . 18 28648255 28648331 DSC2 .. .. 0.160488643 .. .. .. DEL LOW_QUALITY @@ -603,7 +603,6 @@ Sample CV: 0.09 Target CV: 0.10 - #FAQ Which are the criteria of adding a call to the longlist, shortlist or finallist? @@ -635,12 +634,30 @@ All the targets on the X chromosome are of low quality. - Make sure all control samples are of the same gender. +When settig the -zScoreCutOffLow parameter on X I get 'Unknown option :X' + +- If the parameteres in the print to the screen are set correctly the output is correct. However, to prevent the error message instead of a space use an = sign to connect the variable. For instance:\ + +``` +-zScoreCutOffLow=-3 +``` + + -# Changelog v1.2.0 +# Changelog The following bugs have been fixed in the update from version 1.1.6 to v1.2.0: + +##v1.2.1 +- Enabled merging HOM_DEL/HOM_DUP and DEL/DUP calls. Now everything works correctly. + +##v1.2.0.1 +- Disabled merging HOM_DEL/HOM_DUP and DEL/DUP calls as implemented in v1.2.0, because of a bug resulting in showing the start position of the last exon in the call in the longlist instead of the first exon in the call. + +##v1.2.0 + ###Major - In version 1.1.6 after running the StartWithBam function analyzing a region having a coverage of 0, the normalized coverage would have a value of -NaN. This issue is fixed in version 1.2.0, by adding the -a flag to the samtools depth function. However, this causes a dependency on samtools version 1.3 or higher. - In version 1.1.6 HOM_DEL and HOM_DUP calls were interpreted as separate events as DEL and DUP calls. This could cause calls to be cut into several pieces and create gaps in the calls because of downstream filtering. Now, HOM_DEL calls are interpreted as part of a DEL call as well as a separate call. For instance if exons 1 and 3 have a DEL call in the totallist and exon 2 a HOM_DEL call. A deletion of exons 1 to 3 will be called as well as a homozygous deletion of exon 2. Similarly HOM_DUP events are considered as part of DUP events as well as a separate call. Note that in case all targets of a call are considered HOM_DEL or HOM_DUP the call will appear twice on the longlist, shortlist and/or finallist. diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md index 266cb65..cbed0d1 100644 --- a/docs/SUMMARY.md +++ b/docs/SUMMARY.md @@ -9,7 +9,7 @@ * [Test dataset](./README.md#test-dataset) * [QC Thresholds](./README.md#qc-thresholds) * [FAQ](./README.md#faq) - * [Changelog](./README.md#changelog-v1.2.0) + * [Changelog](./README.md#changelog) * [Literature](./README.md#literature) * [Tutorial](./README.md#tutorial) * [Contact](./README.md#contact)