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Virmid — Mon, 12 May 2014 23:16:31 -0000

--- v44
+++ v45
@@ -10,7 +10,13 @@
 .
 .

-## Update note (Last updated 11-7-2013)
+## Update note (Last updated 05-12-2014)
+
+###Virmid-1.1.1 (05-12-2014) *Minor Update
+** Bug fixes: **
+1. Better handling of directory paths for Windows users.
+2. Changes to the header of the VCF files.
+

 ###Virmid-1.1.0 (11-7-2013) *Major update.
 ** Bug fixes:**

Home modified by Virmid

Virmid — Fri, 08 Nov 2013 08:26:01 -0000

--- v43
+++ v44
@@ -117,9 +117,11 @@
 |t|1|Maximal number of thread for multiprocessing. Currently the actual performance is not significantly increased (discouraged to use)|
 |p|10000000|Maximum number of sampling points for training prior probabilities of genotype.|
 |q|0|Minimum mapping quality for sampling point selection. Read with worse mapping quality than this will not be used to sample impurity inference |
-|c|null|Minimum depth of coverage for sampling point selection. Genomic positions with read depth less than this will not be used to sample impurity inference. This option is exclusively used with -v |
-|C|null|Maximum depth of coverage for sampling point. This option can prevent incorrect sample impurity information resulted from other events such as copy number variation or ambiguous mapping. This option is exclusively used with -v|
-|v|2|Maximum fold change of read depth allowed for sampling point. Genomic positions with read depth bigger than or less than the MeanCoverage±StandardDeviation*v will be ignored for impurity inference. This option is exclusively used with -c and -C|
+|c1|null|Minimum depth of coverage for sampling point selection in normal sample. Genomic positions with read depth less than this will not be used to sample impurity inference. This option is exclusively used with -v |
+|C1|null|Maximum depth of coverage for sampling point in normal sample. This option can prevent incorrect sample impurity information resulted from other events such as copy number variation or ambiguous mapping. This option is exclusively used with -v|
+|c2|null|Minimum depth of coverage for sampling point selection in disease sample. Genomic positions with read depth less than this will not be used to sample impurity inference. This option is exclusively used with -v |
+|C2|null|Maximum depth of coverage for sampling point in disease sample. This option can prevent incorrect sample impurity information resulted from other events such as copy number variation or ambiguous mapping. This option is exclusively used with -v|
+|v|null|Maximum fold change of read depth allowed for sampling point. Genomic positions with read depth bigger than or less than the MeanCoverage±StandardDeviation*v will be ignored for impurity inference. This option is exclusively used with -c and -C|

 ##Examples:
     java -jar Virmid.jar -R hg19.fa -D tumor.bam -N normal.bam -c1 20 -C1 100 -c2 20 -C2 100

Home modified by Virmid

Virmid — Thu, 07 Nov 2013 23:43:32 -0000

--- v42
+++ v43
@@ -19,7 +19,7 @@
 3. A few minor bugs including unnecessary dot printing, typos in result files have been fixed.

 ** Changes **
-1. -c/C options have been changed to -c1/C1/c2/C2 options to give a separated parameteres for coverage limit. 'c' is used for minimum coverage, 'C' is for maximum coverage, '1' is for normal and '2' is for disease sample. So 'c1' limits minimum coverage for normal sample, 'C1' limits maximum coverage for normal sample, 'c2' for mimumum disease and 'C2' for maximum disease sample. -c/C options have been deprecated.
+1. -c/C options have been changed to -c1/C1/c2/C2 options to give a separated parameters for coverage limit. 'c' is used for minimum coverage, 'C' is for maximum coverage, '1' is for normal and '2' is for disease sample. So 'c1' limits minimum coverage for normal sample, 'C1' limits maximum coverage for normal sample, 'c2' for mimumum disease and 'C2' for maximum disease sample. -c/C options have been deprecated.
 2. A new parameter '-M' has been applied to control the "maximum considered read depth for each nucletide in variant calling". This is originally introduced to prevent unexpected memery errors or time delays that result from some abnormal regions; due to several reasons, some regions have been read for >10000 times. The default value for 'M' is 500, which means for each nucleotide at most 500 reads are considered to call variants (usually this is enough). But you can always increase the limit, or make it unlimited (give -1 for M).
 3. The output file names are now ".vcf". 
 4. Results are now separated in two different files - 'all' and 'passed'. The 'all' files are same with previous version. The 'passed' files only contain entries that passed all the virmid filters.  
@@ -77,14 +77,15 @@

 Sampling options:

-    -p INT      maximum number of sampling points for training [10000000]
-    -q INT      minimum mapping quality for sampling points [null]
+    -p  INT      maximum number of sampling points for training [10000000]
+    -q  INT      minimum mapping quality for sampling points [null]
     -c1 INT     minimum depth of coverage for normal sampling points [null]. exclusive use with -v
     -C1 INT     maximum depth of coverage for normal sampling points [null]. exclusive use with -v
     -c2 INT     minimum depth of coverage for disease sampling points [null]. exclusive use with -v
     -C2 INT     maximum depth of coverage for disease sampling points [null]. exclusive use with -v
     -v FLOAT    fold of standard deviation for sampling points [0]. exclusive use with -c/-C.
-    -G FLOAT    minimum GMS score for sampling [null]
+    -M  INT     maximum read-depth for consideration in each nucleotide [500] (-1 for unlimited).
+

 Output options:

Home modified by Virmid

Virmid — Thu, 07 Nov 2013 23:41:21 -0000

--- v41
+++ v42
@@ -69,7 +69,6 @@
 Input options:

     -w PATH     working directory [directory of disease input]
-    -g PATH     path for tabix indexed gms files (required -G)
     -a          exit after estimating alpha [false]
     -f          do not reuse previous calls/trained models [false]
     -r INT      read length [Virmid's guess]
@@ -80,9 +79,11 @@

     -p INT      maximum number of sampling points for training [10000000]
     -q INT      minimum mapping quality for sampling points [null]
-    -c INT      minimum depth of coverage for sampling points [null]. exclusive use with -v
-    -C INT      maximum depth of coverage for sampling points [null]. execlusive use with -v
-    -v FLOAT    fold of standard deviation for sampling points [2]. exclusive use with -c/-C.
+    -c1 INT     minimum depth of coverage for normal sampling points [null]. exclusive use with -v
+    -C1 INT     maximum depth of coverage for normal sampling points [null]. exclusive use with -v
+    -c2 INT     minimum depth of coverage for disease sampling points [null]. exclusive use with -v
+    -C2 INT     maximum depth of coverage for disease sampling points [null]. exclusive use with -v
+    -v FLOAT    fold of standard deviation for sampling points [0]. exclusive use with -c/-C.
     -G FLOAT    minimum GMS score for sampling [null]

 Output options:
@@ -120,7 +121,7 @@
 |v|2|Maximum fold change of read depth allowed for sampling point. Genomic positions with read depth bigger than or less than the MeanCoverage±StandardDeviation*v will be ignored for impurity inference. This option is exclusively used with -c and -C|

 ##Examples:
-    java -jar Virmid.jar -R hg19.fa -D tumor.bam -N normal.bam -c 20 -C 100
+    java -jar Virmid.jar -R hg19.fa -D tumor.bam -N normal.bam -c1 20 -C1 100 -c2 20 -C2 100
 will find all somatic mutations between tumor.bam and normal.bam based on hg19 assembly. Positions with read depth less than 20 and more than 100 will be ignored for sample impurity inference.

     java -jar Virmid.jar -R Homo_Sapiens_assembly19.fasta -D brain.bam -N blood.bam -v 3 -af
@@ -130,12 +131,12 @@

 Virmid outputs the following output files:

-1. **$DiseaseSampleName.virmid.som**
-:    List of somatic mutation found by Virmid. The output format is standard VCF4.1.
-2. **$DiseaseSampleName.virmid.loh**
-:    List of loss of heterozygosity found by Virmid. This is also in VCF4.1 format.
-3. **$DiseaseSampleName.virmid.germ**
-:    List of germline variations found by Virmid in VCF4.1 format
+1. **$DiseaseSampleName.virmid.som.all.vcf**, **$DiseaseSampleName.virmid.som.passed.vcf**
+:    List of (filtered) somatic mutation found by Virmid. The output format is standard VCF4.1.
+2. **$DiseaseSampleName.virmid.loh.all.vcf**, **$DiseaseSampleName.virmid.loh.passed.vcf**
+:    List of (filtered) loss of heterozygosity found by Virmid. This is also in VCF4.1 format.
+3. **$DiseaseSampleName.virmid.germ.all.vcf**, **$DiseaseSampleName.virmid.germ.passed.vcf**
+:    List of (filtered) germline variations found by Virmid in VCF4.1 format
 3. **$DiseaseSampleName.virmid.report**
 :    Report of basic information in the Virmid running including used parameters, input files, intermediate results, and output destination.

@@ -192,27 +193,36 @@
 ##Report file
 Virmid outputs .virmid.report file for each run. This contains basic information of the run including estimated impurity (alpha) and the locations of final outputs.

-    # Running Virmid ver 0.1
+    # Running Virmid ver 1.1.0
     # Parameters in this run.
-    Input Files:
-            Disease sample: Tumor.sort_mapped_realign_mdup_recal.bam
-            Normal sample: Normal.sort_mapped_realign_mdup_recal.bam
-            Reference genome: hg19.fa
-    Input parameters:
-            Read Length: 100
-            Maximum coverage for sampling: 200
-            Minimum coverage for sampling: 20
-            Minimum mapping quality for sampling: 17
-    Output parameters:
-            Working directory: /data/
-            Report file: /data/Tumor.sort_mapped_realign_mdup_recal.bam.virmid.report
-    
-    Estimated alpha: 0.8885117716338826
-    Output files:
-            Somatic mutations: /data/Tumor.sort_mapped_realign_mdup_recal.bam.virmid.som
-            Germline mutations: /data/Tumor.sort_mapped_realign_mdup_recal.bam.virmid.germ
-            Loss of heterozygosity: /data/Tumor.sort_mapped_realign_mdup_recal.bam.virmid.loh
-
+Input Files:
+        Disease sample: 2341T_recal.bam
+                Mean Coverage: 72.01583333333348
+                Coverage Standard Deviation: 90.1898035603241
+        Normal sample: 2341G_recal.bam
+                Mean Coverage: 36.41749999999998
+                Coverage Standard Deviation: 45.896614636571385
+        Reference genome: hg19.fa
+Input parameters:
+        Read Length: 100
+        Maximum coverage for disease sampling: 120
+        Minimum coverage for disease sampling: 20
+        Maximum coverage for normal sampling: 100
+        Minimum coverage for normal sampling: 10
+        Minimum mapping quality for sampling: 17
+Output parameters:
+        Working directory: /data/test/
+        Report file: /data/test/2341T_recal.bam.virmid.report
+
+Estimated alpha: 0.6687711902178711
+
+Output files:
+        All somatic mutations: /data/test/2341T_recal.bam.virmid.som.all.vcf
+        Filtered somatic mutations: /data/test/2341T_recal.bam.virmid.som.passed.vcf
+        All germline mutations: /data/test/2341T_recal.bam.virmid.germ.all.vcf
+        Filtered germline mutations: /data/test/2341T_recal.bam.virmid.germ.passed.vcf
+        All loss of heterozygosity: /data/test/2341T_recal.bam.virmid.loh.all.vcf
+        Filtered loss of heterozygosity: /data/test/2341T_recal.bam.virmid.loh.passed.vcf

 [1000 genomes webpage]: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

Home modified by Virmid

Virmid — Thu, 07 Nov 2013 23:27:06 -0000

--- v40
+++ v41
@@ -9,9 +9,22 @@

 .
 .
-## Recent changes (Last updated 5-29-2013)
-Virmid-1.0.2 has been updated. 
-
+
+## Update note (Last updated 11-7-2013)
+
+###Virmid-1.1.0 (11-7-2013) *Major update.
+** Bug fixes:**
+1. A major bug with '-v' option has been fixed. (Please note that using mean/stdev coverage for sampling is discouraged in exome sequencing due to the large standard deviation)
+2. A major bug related to extremely high coverage regions has been fixed. 
+3. A few minor bugs including unnecessary dot printing, typos in result files have been fixed. 
+
+** Changes **
+1. -c/C options have been changed to -c1/C1/c2/C2 options to give a separated parameteres for coverage limit. 'c' is used for minimum coverage, 'C' is for maximum coverage, '1' is for normal and '2' is for disease sample. So 'c1' limits minimum coverage for normal sample, 'C1' limits maximum coverage for normal sample, 'c2' for mimumum disease and 'C2' for maximum disease sample. -c/C options have been deprecated.
+2. A new parameter '-M' has been applied to control the "maximum considered read depth for each nucletide in variant calling". This is originally introduced to prevent unexpected memery errors or time delays that result from some abnormal regions; due to several reasons, some regions have been read for >10000 times. The default value for 'M' is 500, which means for each nucleotide at most 500 reads are considered to call variants (usually this is enough). But you can always increase the limit, or make it unlimited (give -1 for M).
+3. The output file names are now ".vcf". 
+4. Results are now separated in two different files - 'all' and 'passed'. The 'all' files are same with previous version. The 'passed' files only contain entries that passed all the virmid filters.  
+
+###Virmid-1.0.2 (5-29-2013)

 **Bug fixes:**
 1. There was a bug with '-w' (setting working directory) option. (We thank Dr. Malachi Griffith in WUSTL!)

Home modified by Virmid

Virmid — Fri, 31 May 2013 23:58:52 -0000

--- v39
+++ v40
@@ -11,11 +11,15 @@
 .
 ## Recent changes (Last updated 5-29-2013)
 Virmid-1.0.2 has been updated. 
-Bug fixes:
+
+
+**Bug fixes:**
 1. There was a bug with '-w' (setting working directory) option. (We thank Dr. Malachi Griffith in WUSTL!)
 2. There was a problem with saving sampling positions to BAM files.
 3. There was a minor bug in determining indel proximity of the sampled position.
-Others:
+
+
+**Other improvements:**
 1. There was a slight speed improvement.
 2. Now, predicted genotypes for germline mutations are written in the final output. The ID in the VCF file is 'gt', and it has 'h'(heterozygous) or 'H'(Homozygous) followed by the probability of the genotype.

@@ -24,7 +28,7 @@

 Virmid was developed using JAVA JDK 7 64bit. To run Virmid, Java Runtime Environment (JRE) version 1.7.x or later is required. Download the most recent version of virmid program in the code page and extract the gzipped archive.

-    tar -zxvf virmid-1.x.tar.gz
+    tar -zxvf virmid-1.x.y.tar.gz

 It will generate a new directory virmid-1.x, which contains the followings:

Home modified by Virmid

Virmid — Thu, 30 May 2013 01:50:09 -0000

--- v38
+++ v39
@@ -12,7 +12,7 @@
 ## Recent changes (Last updated 5-29-2013)
 Virmid-1.0.2 has been updated. 
 Bug fixes:
-1. There was a bug with '-w' (setting working directory) option.
+1. There was a bug with '-w' (setting working directory) option. (We thank Dr. Malachi Griffith in WUSTL!)
 2. There was a problem with saving sampling positions to BAM files.
 3. There was a minor bug in determining indel proximity of the sampled position.
 Others:

Home modified by Virmid

Virmid — Thu, 30 May 2013 01:48:44 -0000

--- v37
+++ v38
@@ -9,8 +9,8 @@

 .
 .
-## Recent changes
-Virmid-1.0.2 has been updated (5/29/13). 
+## Recent changes (Last updated 5-29-2013)
+Virmid-1.0.2 has been updated. 
 Bug fixes:
 1. There was a bug with '-w' (setting working directory) option.
 2. There was a problem with saving sampling positions to BAM files.

Home modified by Virmid

Virmid — Thu, 30 May 2013 01:48:08 -0000

--- v36
+++ v37
@@ -9,6 +9,17 @@

 .
 .
+## Recent changes
+Virmid-1.0.2 has been updated (5/29/13). 
+Bug fixes:
+1. There was a bug with '-w' (setting working directory) option.
+2. There was a problem with saving sampling positions to BAM files.
+3. There was a minor bug in determining indel proximity of the sampled position.
+Others:
+1. There was a slight speed improvement.
+2. Now, predicted genotypes for germline mutations are written in the final output. The ID in the VCF file is 'gt', and it has 'h'(heterozygous) or 'H'(Homozygous) followed by the probability of the genotype.
+  
+
 #Installation of Virmid

 Virmid was developed using JAVA JDK 7 64bit. To run Virmid, Java Runtime Environment (JRE) version 1.7.x or later is required. Download the most recent version of virmid program in the code page and extract the gzipped archive.

Home modified by Virmid

Virmid — Fri, 03 May 2013 22:28:08 -0000

--- v35
+++ v36
@@ -20,7 +20,7 @@
 1. **Virmid.jar**
 :    executable JAR file of Virmid
 2. **README.TXT**
-:    Virmid manual 
+:    Nothing much in this file currently. Please refer to this page instead.
 3. **lib/**
 :    directory containing other JAR libraries for Virmid

@@ -108,14 +108,14 @@
 :    List of loss of heterozygosity found by Virmid. This is also in VCF4.1 format.
 3. **$DiseaseSampleName.virmid.germ**
 :    List of germline variations found by Virmid in VCF4.1 format
-3. **$DiseaseSampleName.report**
+3. **$DiseaseSampleName.virmid.report**
 :    Report of basic information in the Virmid running including used parameters, input files, intermediate results, and output destination.

 The following files are generated by Virmid for its internal use:

 1. **$DiseaseSampleName.virmid.sample.control.bam and **$DiseaseSampleName.virmid.sample.disease.bam**
 :    BAM files of selected positions for sample impurity inference. Virmid automatically tries to find these files to speed up the running. When these file do not exist (e.g. first time running) or Virmid was ran with -f option, Virmid will try to generated these files again.
-2. **$DiseaseSampleName.virmi2.gm**
+2. **$DiseaseSampleName.virmid2.gm**
 :    A saved matrix of joint genotype matrix. Virmid will also try to used this for faster running. This file will be also ignored by -f option.

 ##The VCF file