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Updates to processing performed
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@mwyczalkowski
mwyczalkowski committed Sep 21, 2022
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44 changes: 22 additions & 22 deletions DCC_Analysis_Summary/README.Y3.md
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Last updated: 5/17/21
Last updated: 9/20/21

**BOLD** are new since 4/20/22
**BOLD** are new since 5/18/22

## Analysis Summaries - Case counts - Y3 only
Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
--- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
Methylation Array | 115 | 260 | 8 | 205 | 111 | 202 | 229 | 164 | 19 | 249 | 1562
miRNA-Seq | 83 | 82 | 3 |239| 22 | 104 | 72 | 164 | 0 | 35 | 804
RNA-Seq Expression | 101 | 261 | 8 | 189 | 111 | 202 | 229 | 186 | 19 | 252 | 1558
RNA-Seq Fusion | 171 | 110 | 0 |116| 0 | 89 | 109 | 81 | 0 | 170 | 846
RNA-Seq Transcript + Splicing | 172 | 149 | 0 | 136 | 0 | 89 | 208 | 103 | 0 | 170 | 1027
WGS CNV Somatic | 29 | 258 | 0 | 187 | 111 | 202 | 219 | 166 | 0 | 243 | 1415
WGS SV | 35 | 258 | 0 | 129 | 111 | 173 | 109 | 108 | 0 | 204 | 1218
WXS MSI | 42 | 193 | 0 | 71 | 0 | 89 | 108 | 166 | 0 | 104 | 773
WXS Somatic TD | 42 | 259 | 0 | 185 | 111 | 202 | 218 | 181 | 0 | 233 | 1443
WXS Somatic SW | **42** | 260 | 0 | 185 | 111 | 202 | 110 | 181 | 0 | 247 |**1338**
WXS Germline | 42 | 259 | 0 | 186 | 111 | 199 |229| 166 | 0 | 233 | 1425
miRNA-Seq |**172**|82 | 3 |**249**| 22 | 104 | 72 | 164 | 0 | 35 | **903**
RNA-Seq Expression |**172**|261 | 8 |**243**| 111 | 202 | 229 | 186 | 19 | 252 |**1683**
RNA-Seq Fusion |**172**| 110 | 0 |**127**| 0 | 89 | 109 | 81 | 0 | 170 | **858**
RNA-Seq Transcript + Splicing | 172 | 149 | 0 |**146**| 0 | 89 | 208 | 103 | 0 | 170 |**1037**
WGS CNV Somatic |**133**| 258 | 0 |**218**| 111 | 202 | 219 | 166 | 0 | 243 |**1550**
WGS SV |**139**| 258 | 0 |**160**| 111 | 173 | 109 | 108 | 0 | 204 |**1353**
WXS MSI |**160**| 193 | 0 |**112**| 0 | 89 | 108 | 166 | 0 | 104 |**932**
WXS Somatic TD |**160**| 259 | 0 |**225**| 111 | 202 | 218 | 181 | 0 | 233 |**1601**
WXS Somatic SW |**160**| 260 | 0 |**225**| 111 | 202 | 110 | 181 | 0 | 247 |**1496**
WXS Germline |**160**| 259 | 0 |**230**| 111 | 199 |229| 166 | 0 | 233 |**1587**

<!-- Note, WXS Somatic CCRCC was not reported to DCC analysis summary -->
## All results (Y1, Y2, Y3) - Case counts

Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
--- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
Methylation Array | 115 | 260 | 8 | 205 | 111 | 202 | 229 | 164 | 19 | 249 | 1562
miRNA-Seq | 83 | 261 | 8 | 239 | 111 | 202 | 229 | 164 | 19 | 250 | 1566
RNA-Seq Expression | 101 | 261 | 8 | 189 | 111 | 202 | 229 | 186 | 19 | 252 | 1558
RNA-Seq Fusion | 171 | 222 | 8 | 234 | 111 | 202 | 229 | 164 | 19 | 246 | 1606
RNA-Seq Transcript + Splicing | 172 | 261 | 3 | 234 | 111 | 202 | 218 | 186 | 0 | 246 | 1633
WGS CNV Somatic | 29 | 258 | 0 | 187 | 111 | 202 | 229 | 166 | 0 | 243 | 1425
WGS SV | 35 | 258 | 0 | 187 | 111 | 201 | 219 | 166 | 0 | 243 | 1511
WXS MSI | 42 | 259 | 0 | 188 | 111 | 202 | 219 | 166 | 0 | 247 | 1434
WXS Somatic TD | 42 | 259 | 0 | 185 | 111 | 202 | 218 | 181 | 0 | 233 | 1443
WXS Somatic SW | 42 | 260 | 0 | 185 | 111 | 202 | 218 | 181 | 0 | 247 | 1446
WXS Germline | 42 | 259 | 0 | 186 | 111 | 199 | 229 | 166 | 0 | 233 | 1425
miRNA-Seq | 172 | 261 | 8 | 249 | 111 | 202 | 229 | 164 | 19 | 250 | 1665
RNA-Seq Expression | 172 | 261 | 8 | 243 | 111 | 202 | 229 | 186 | 19 | 252 | 1683
RNA-Seq Fusion | 172 | 222 | 8 | 243 | 111 | 202 | 229 | 164 | 19 | 246 | 1616
RNA-Seq Transcript + Splicing | 172 | 261 | 3 | 244 | 111 | 202 | 218 | 186 | 0 | 246 | 1643
WGS CNV Somatic | 133 | 258 | 0 | 218 | 111 | 202 | 229 | 166 | 0 | 243 | 1560
WGS SV | 139 | 258 | 0 | 218 | 111 | 201 | 219 | 166 | 0 | 243 | 1646
WXS MSI | 160 | 259 | 0 | 228 | 111 | 202 | 219 | 166 | 0 | 247 | 1543
WXS Somatic TD | 160 | 259 | 0 | 225 | 111 | 202 | 218 | 181 | 0 | 233 | 1601
WXS Somatic SW | 160 | 260 | 0 | 225 | 111 | 202 | 218 | 181 | 0 | 247 | 1604
WXS Germline | 160 | 259 | 0 | 230 | 111 | 199 | 229 | 166 | 0 | 233 | 1587

<!-- Note - TD numbers don't add up... -->

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2 changes: 2 additions & 0 deletions DCC_Analysis_Summary/src/DCC_case_counts.sh
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Expand Up @@ -93,6 +93,7 @@ fi
# Complication comes up when case has name like `C3L-00103.HET_oymKX`
# This is strictly incorrect, but is used to keep the run name unique
# in this case, need to strip off the .HET... to get at the real case name
# This is a bit of a mess. Much better to fix up the case names
FILTER_CASE="awk 'BEGIN{FS=\"\t\";OFS=\"\t\"}{print substr(\$1,1,9), \$2, \$3}'"
echo $DAS
echo Cases per disease
Expand All @@ -101,6 +102,7 @@ echo Cases per disease
# Above is incorrect, since this double-counts case if processed in more than one year
# Merge by year (retain case only once even if processed multiple years)
CMD="cut -f 1,2,6 $DAS | $FILTER | $FILTER_CASE | cut -f 1,2 | sort -u | cut -f 2 | sort | uniq -c"
#CMD="cut -f 1,2,6 $DAS | $FILTER | cut -f 1,2 | sort -u | cut -f 2 | sort | uniq -c"
echo Running: $CMD
eval $CMD

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