Some sample_id and aliquot_id in histologies.tsv are mis-coded

[jharenza]

What data file(s) does this issue pertain to?

histologies.tsv

What release are you using?

v7

Put your question or report your issue here.

Some TARGET samples have sample_id == 03, while their corresponding TARGET ids (in Kids_First_Biospecimen_ID) contain other ids indicative of sample ids. Similarly, these samples have the wrong aliquot_id:

> v7 %>%
+   filter(cohort == "TARGET" & sample_id == "03") %>%
+   select(Kids_First_Biospecimen_ID, sample_id, aliquot_id)
# A tibble: 812 x 3
   Kids_First_Biospecimen_ID sample_id aliquot_id
   <chr>                     <chr>     <chr>     
 1 TARGET-50-CAAAAQ-01A-01R  03        02        
 2 TARGET-50-PALJIP-02A-01R  03        02        
 3 TARGET-50-PALFME-02A-01R  03        02        
 4 TARGET-50-PAJNLT-01A-01R  03        02        
 5 TARGET-50-PAKKSE-01A-01R  03        02        
 6 TARGET-50-PAJNCJ-01A-01R  03        02        
 7 TARGET-50-PAKRVH-01A-01R  03        02        
 8 TARGET-50-PAJMKJ-01A-01R  03        02        
 9 TARGET-50-PAECJB-01A-01R  03        02        
10 TARGET-50-PAKFME-01A-01R  03        02        
# … with 802 more rows

Please double check logic for all TARGET ids.

[jharenza]

cc @migbro

@ewafula when you have a fix for this posted to the D3b-codes repo, can you mention that here and let @migbro know - he can then use the updated file for the pedcbio load mentioned in #118

[ewafula]

Sure, will before the end the day.

…

On Fri, Jul 30, 2021 at 4:09 PM Jo Lynne Rokita ***@***.***> wrote: cc @migbro <https://github.com/migbro> @ewafula <https://github.com/ewafula> when you have a fix for this posted to the D3b-codes repo, can you mention that here and let @migbro <https://github.com/migbro> know - he can then use the updated file for the pedcbio load mentioned in #118 <#118> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZN26DNCXBRDHC5IMFGGWLT2MBGXANCNFSM5BJEQ6EQ> .

[runjin326]

Close with PR89