Final polish

lessons/10_variant_prioritization.md

@@ -65,7 +65,7 @@ Let's break down the syntax a bit:
 
 
 > #### Revisiting "( FILTER = 'PASS' )"
-> Recall that we had used `SnpSift`, in the [filtering command that we used earlier](08_variant_filtering.md#filter-using-snpsift) in the workshop. In that lesson we used `SnpSift`to look at the `FILTER` field and reatin varaints with the value of `PASS`.
+> Recall that we had used `SnpSift`, in the [filtering command that we used earlier](08_variant_filtering.md#filter-using-snpsift) in the workshop. In that lesson we used `SnpSift`to look at the `FILTER` field and retain varaints with the value of `PASS`.
 > 
 > ```
 > # YOU DO NOT NEED TO RUN THIS
@@ -114,7 +114,7 @@ java -jar $SNPEFF/SnpSift.jar filter \
 
 To filter by the gene name you will need `"( ANN[*].GENE = 'INSERT_GENE_NAME' )"`. 
 
-> NOTE: When handling multiple valued fields (i.e. fields with commas), `SnpSift` uses a 0-based index to describing those elements. In the example below, we can see that the first four `ANN` fields are for the gene `CPTP` before we get to the annotations for `CPSF3L`. So instead if you have used `"( ANN[0].GENE = 'CPSF3L' )"` instead of `"( ANN[*].GENE = 'CPSF3L' )"`, then it will only return the entries which have `"CPSF3L"` in the first `GENE` annotation field and exclude the example below. The `*` tell `SnpSift` to extract the record if "any" annotations corresponds to `CPSF3L`. For most cases, you will want to use the `*`, but you should understand why it is there.
+> NOTE: When handling multiple valued fields (i.e. fields with commas), `SnpSift` uses a 0-based index to describing those elements. In the example below, we can see that the first four `ANN` fields are for the gene `CPTP` before we get to the annotations for `CPSF3L`. So if you used `"( ANN[0].GENE = 'CPSF3L' )"` instead of `"( ANN[*].GENE = 'CPSF3L' )"`, then it will only return the entries which have `"CPSF3L"` in the first `GENE` annotation field and exclude the later entries. The `*` tells `SnpSift` to extract the record if "any" annotations corresponds to `CPSF3L`. For most cases, you will want to use the `*`, but you should understand why it is there.
 > ```
 > 1       1324300 .       G       A       .       PASS    AS_FilterStatus=SITE;AS_SB_TABLE=47,6|11,0;ClippingRankSum=0.39;DP=68;ECNT=1;FS=2.373;GERMQ=93;MBQ=27,27;MFRL=337,338;MMQ=60,60;MPOS=27;MQ=60;MQ0=0;MQRankSum=0;NALOD=1.54;NLOD=9.88;POPAF=6;ReadPosRankSum=-0.125;TLOD=24.65;ANN=A|upstream_gene_variant|MODIFIER|CPTP|CPTP|transcript|NM_001029885.1|protein_coding||c.-2611G>A|||||463|,A|upstream_gene_variant|MODIFIER|CPTP|CPTP|transcript|XM_005244802.1|protein_coding||c.-3008G>A|||||456|,A|upstream_gene_variant|MODIFIER|CPTP|CPTP|transcript|XM_005244801.3|protein_coding||c.-2611G>A|||||843|,A|upstream_gene_variant|MODIFIER|CPTP|CPTP|transcript|XM_011542200.2|protein_coding||c.-2611G>A|||||1315|,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|XM_011541647.1|protein_coding|1/18|c.28+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|NM_001256456.1|protein_coding|1/18|c.-428+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|NM_001256460.1|protein_coding|1/17|c.-167+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|NM_001256462.1|protein_coding|1/14|c.28+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|NM_001256463.1|protein_coding|1/14|c.28+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|NM_017871.5|protein_coding|1/16|c.28+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|XM_017001558.1|protein_coding|1/18|c.-438+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|XM_017001557.1|protein_coding|1/17|c.-361+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|XM_011541648.1|protein_coding|1/18|c.-91+281C>T||||||,A|intron_variant|MODIFIER|CPSF3L|CPSF3L|transcript|XM_011541650.1|protein_coding|1/16|c.-254+281C>T||||||  GT:AD:AF:DP:F1R2:F2R1:SB        0/0:33,0:0.028:33:12,0:20,0:32,1,0,0    0/1:20,11:0.367:31:6,6:12,5:15,5,11,0
 > ```
@@ -129,6 +129,19 @@ java -jar $SNPEFF/SnpSift.jar filter \
 
 ### INFO Field: Effects
 
+If you want to filter your output by the effects the variants have on the annotated gene models, the syntax for this is quite similar to the example for genes:
+
+```
+java -jar $SNPEFF/SnpSift.jar filter \
+  -noLog \
+  "( ANN[*].EFFECT has 'missense_variant' )" \
+  mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  | less
+```
+
+To filter by a variant effect, the filter syntax is `"( ANN[*].EFFECT has 'VARIANT_EFFECT' )"`
+
+> **NOTE**: Importantly, notice the use of `has` instead of `=` here. Sometimes effects field will contain mutliple effects such as `missense_variant&splice_donor_variant`. Using `ANN[*].EFFECT = missense_variant` here ***WILL NOT*** return this line, because the line is not equal to `missense_variant`, however `ANN[*].EFFECT has missense_variant` ***WILL*** return this line. Oftentimes for effects, one would be interested in the `has` query as opposed to the `=` one.
+
 There are many different variant effects and some of the more common ones are listed below:
 
 | SnpEff Annotation | Type of variant |
@@ -147,36 +160,23 @@ There are many different variant effects and some of the more common ones are li
 
 Many more effects can be found [here](https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details).
 
-If you want to filter your output by the effects the variants have on the annotated gene models, the syntax for this is quite similar to the example for genes:
-
-```
-java -jar $SNPEFF/SnpSift.jar filter \
-  -noLog \
-  "( ANN[*].EFFECT has 'missense_variant' )" \
-  mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  | less
-```
-
-To filter by a variant effect, the filter syntax is `"( ANN[*].EFFECT has 'VARIANT_EFFECT' )"`
-
-> **NOTE**: Importantly, notice the use of `has` instead of `=` here. Sometimes effects field will contain mutliple effects such as `missense_variant&splice_donor_variant`. Using `ANN[*].EFFECT = missense_variant` here ***WILL NOT*** return this line, because the line is not equal to `missense_variant`, however `ANN[*].EFFECT has missense_variant` ***WILL*** return this line. Oftentimes for effects, one would be interested in the `has` query as opposed to the `=` one.
-
-
 ### INFO Field: Impacts
 
 `SnpEff` also predicts the deleterious nature of a variant by binning it into one of several categories:
 
 - `HIGH` These are variants that will **almost certainly have a deleterious impact on the transcript**. Examples of this would be the loss or gain of a stop codon or a frameshift mutation. 
 - `MODERATE` These are variants where the impact may have a deleterious impact on the transcript. Examples of this would be missense/non-synonymous variants and in-frame deletions/insertions.
 - `LOW` These are variants that are **unlikely to have a deleterious impact on the transcript**. Examples of this would be silent/synonymous variants and alterations between different stop codons.
-- `MODIFER` These variants are typically in non-coding regions and their impacts are difficult to assertain. 
+- `MODIFER` These variants are typically in non-coding regions and their impacts are difficult to ascertain. 
 
-More information on these categories can be found [here](https://pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction) and a complete listing of the categories for each effect can be found [here](https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details). 
+More information on these categories can be found [here](https://pcingola.github.io/SnpEff/snpeff/inputoutput/#impact-prediction) and a complete listing of the categories for each effect can be found [here](https://pcingola.github.io/SnpEff/snpeff/inputoutput/#effect-prediction-details). 
 
 Let's go ahead and select out all of our `HIGH` impact muations:
 
 ```
 java -jar $SNPEFF/SnpSift.jar filter \
-  -noLog "( ANN[*].IMPACT has 'HIGH' )" \
+  -noLog \
+  "( ANN[*].IMPACT has 'HIGH' )" \
   mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  | less
 ```
 
@@ -186,19 +186,19 @@ Let's go ahead and redirect the output of these "high-impact" mutations to a new
 
 ```
 java -jar $SNPEFF/SnpSift.jar filter \
-  -noLog "( ANN[*].IMPACT has 'HIGH' )"  \
+  -noLog \
+  "( ANN[*].IMPACT has 'HIGH' )"  \
   mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  > mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.high_impact.vcf 
 ```
 
 ### INFO: Other ANN fields
 
-In addition to `GENE`, `EFFECT` and `IMPACT`, there are a whole host of other `ANN` fields. Some of the other `ANN` fields that we will come across later are:
+In addition to `GENE`, `EFFECT`, `IMPACT` AND `TRID`, there are a whole host of other `ANN` fields. Some of the other `ANN` fields that we will come across later are:
 
-- `TRID` - Transcript ID or NCBI accesssion number
 - `HGVS_P` - The alteration in protein notation
 - `HGVS_C` - The alteration in DNA notation
 
-A full list of `ANN` fields can be found [here](http://pcingola.github.io/SnpEff/ss_filter/#snpeff-ann-fields).
+A full list of `ANN` fields can be found [here](https://pcingola.github.io/SnpEff/snpsift/filter/#snpeff-ann-fields).
 
 ## Snpsift: `vcfEffOnePerLine`
 
@@ -256,7 +256,7 @@ Let's breakdown this command:
 - `-noLog` This does not report command usage to `SnpEff`'s server
 - `"( ANN[*].EFFECT has 'missense_variant' )"` Filter out lines where `missense_variant` is annotation in ***ANY*** annotation.
 - `mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf |` This is our input file and then pipe this output.
-- `$SNPEFF/scripts/vcfEffOnePerLine.pl` Place each effect on it's own line and pipe this output.
+- `$SNPEFF/scripts/vcfEffOnePerLine.pl |` Place each effect on it's own line and pipe this output.
 - `java -jar $SNPEFF/SnpSift.jar extractFields` This calls the `extractFields` package within `SnpSift`
 - `-` The use of `-` is very commonly used to define the input as coming from standard input, or in other words, the input is being piped into the command. 
 - `"CHROM" "POS" "ANN[*].GENE" "ANN[*].TRID" "EFF[*].HGVS_P" "ANN[*].HGVS_C" "ANN[*].EFFECT"` This is defining the fields that we would like to filter.