Comments (4)
congzhouczcz
commented on July 24, 2024
What is the format of file 'pop to use as root' and 'pop to use as anc' ?
Thanks very much!
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grenaud
commented on July 24, 2024
Hello!
Suppose you have a file with the populations you want to use as outgroup and ancestor. In the case of hominin, it would be the chimp as outgroup and the Chimp/human ancestor as the ancestor. For example I would have the following
file1.acf.gz:
#ACF
#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz
#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#DATE: 2019-12-02
#SQ SN:1 LN:249250621
#SQ SN:2 LN:243199373
#chr coord REF,ALT root anc chimp ChimpHumanAncestor
2 100022 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100023 G,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100024 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100025 C,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100026 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100027 G,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100028 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100029 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100030 C,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100031 T,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100032 T,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100033 C,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100034 A,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100035 T,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100036 T,N 0,0:0 0,0:0 1,0:0 1,0:0
2 100037 G,N 0,0:0 0,0:0 1,0:0 1,0:0
And I would have a second file without root and ancestral information:
file2.acf.gz:
#ACF
#PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz
#GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
#DATE: 2019-12-02
#SQ SN:1 LN:249250621
#SQ SN:2 LN:243199373
#chr coord REF,ALT root anc AltaiNean Denisova FrenchB YorubaB AustralianB
2 100022 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100023 G,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100024 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100025 C,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100026 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100027 G,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100028 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100029 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100030 C,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100031 T,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100032 T,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100033 C,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100034 A,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100035 T,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100036 T,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100037 G,N 0,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
First we will go into file1 and it take our two populations as our root and ancestor and put it into file3.acf.gz:
glactools usepopsrootanc file1.acf.gz chimp ChimpHumanAncestor > file3.acf.gz
file3.acf.gz will look like this:
#ACF
#PG:usepopsrootanc /tmp/temp.acf.gz chimp ChimpHumanAncestor
#GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
#DATE: 2020-04-02
#USEPOPASROOTANC: chimp chimp
#USEPOPASROOTANC#1
# #ACF
# #PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz
# #GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
# #DATE: 2019-12-02
# #chr coord REF,ALT root anc chimp ChimpHumanAncestor
#SQ SN:1 LN:249250621
#SQ SN:2 LN:243199373
#chr coord REF,ALT root anc
2 100022 A,N 1,0:0 1,0:0
2 100023 G,N 1,0:0 1,0:0
2 100024 A,N 1,0:0 1,0:0
2 100025 C,N 1,0:0 1,0:0
2 100026 A,N 1,0:0 1,0:0
2 100027 G,N 1,0:0 1,0:0
2 100028 A,N 1,0:0 1,0:0
2 100029 A,N 1,0:0 1,0:0
2 100030 C,N 1,0:0 1,0:0
2 100031 T,N 1,0:0 1,0:0
2 100032 T,N 1,0:0 1,0:0
2 100033 C,N 1,0:0 1,0:0
2 100034 A,N 1,0:0 1,0:0
2 100035 T,N 1,0:0 1,0:0
2 100036 T,N 1,0:0 1,0:0
2 100037 G,N 1,0:0 1,0:0
Then you can use "replaceanc" to put the ancestral information into file2:
glactools replaceanc file2.acf.gz file3.acf.gz > file4.acf.gz
file4 should contain the same information as file to accept with the ancestral information of file1:
#ACF
#PG:replaceanc /tmp/temp2.acf.gz /tmp/file3.acf.gz
#GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
#DATE: 2020-04-02
#REPLACEANC:
#REPLACEANC#1
# #ACF
# #PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz
# #GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
# #DATE: 2019-12-02
# #chr coord REF,ALT root anc AltaiNean Denisova FrenchB YorubaB AustralianB
#REPLACEANC#2
# #ACF
# #PG:usepopsrootanc /tmp/temp.acf.gz chimp ChimpHumanAncestor
# #GITVERSION: 9d3e4107ea445a16737fb841e2181dabf31acac9
# #DATE: 2020-04-02
# #USEPOPASROOTANC: chimp chimp
# #USEPOPASROOTANC#1
# # #ACF
# # #PG:union AltaiNean.acf.gz Denisova.acf.gz FrenchB.acf.gz YorubaB.acf.gz AustralianB.acf.gz
# # #GITVERSION: 6e48e0efbfb131a6723830fa98f655a36da8c574
# # #DATE: 2019-12-02
# # #chr coord REF,ALT root anc chimp ChimpHumanAncestor
# #chr coord REF,ALT root anc
#SQ SN:1 LN:249250621
#SQ SN:2 LN:243199373
#chr coord REF,ALT root anc AltaiNean Denisova FrenchB YorubaB AustralianB
2 100022 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100023 G,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100024 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100025 C,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100026 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100027 G,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100028 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100029 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100030 C,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100031 T,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100032 T,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100033 C,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100034 A,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100035 T,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100036 T,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
2 100037 G,N 1,0:0 1,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0
In this case I have created two superfluous files, depending on your level of comfort with Unix file descriptors, you can do the same process without creating intermediate files.
Hope this answers your questions, should I add this to the readme? let me know if I can close this issue.
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grenaud
commented on July 24, 2024
Is this fine? Can I close the issue?
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congzhouczcz
commented on July 24, 2024
Thank you very much, grenaud. I get it and now it works.
Thanks!
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