These are chat archives for dereneaton/ipyrad

7th
Aug 2018
yihanwu
@yihanwu
Aug 07 2018 20:50 UTC

Hi @isaacovercast , I seem to have some malformed CATG fields in my vcf file like below

locus_170673    132     .       C       T       13      PASS    NS=78;DP=234973 GT:DP:CATG      0/0:5959:5296,0,663,    0/0:211:203,0,8,0        0/0:2108:1887,9,211,    ./.:0:0,0,0,0   0/0:582:537,0,45,0      0/0:2455:2176,0,279,    0/0:6853:6295,0,558,     0/0:541:486,0,55,0      0/0:5331:4897,0,432,    0/0:7687:7282,0,405,    1/0:74:62,0,12,0        0/0:4471:3947,0,524,     0/0:5681:5355,0,326,    0/0:322:322,0,0,0       0/0:4634:4512,0,122,    ./.:0:0,0,0,0   ./.:0:0,0,0,0   0/0:1947:1903,0,44,0     0/0:287:268,0,19,0      0/0:1318:1258,0,60,0    0/0:1126:1065,0,61,0    0/0:5471:5265,0,206,    0/0:404:387,0,17,0       0/0:1538:1503,1,34,0    0/0:5836:5676,0,160,    0/0:7239:7018,0,221,    0/0:4149:3989,0,160,    0/0:2592:2558,0,34,0     0/0:1231:1196,0,35,0    0/0:39:39,0,0,0 ./.:0:0,0,0,0   0/0:2637:2545,0,92,0    0/0:925:896,0,29,0       0/0:1663:1627,1,35,0    0/0:1094:1059,0,35,0    0/0:2211:2122,1,88,0    0/0:7363:7189,0,174,    0/0:3146:3012,0,134,     0/0:4136:4040,0,96,0    ./.:0:0,0,0,0   ./.:22:18,0,4,0 0/0:6160:6073,0,87,0    0/0:5036:4870,0,166,    0/0:1888:1835,0,53,0     0/0:3068:2977,0,91,0    0/0:2919:2885,0,34,0    0/0:8561:8338,0,223,    0/0:82:82,0,0,0 0/0:864:844,4,16,0       0/0:5128:5033,0,95,0    0/0:5199:4987,0,212,    0/0:9976:9735,0,241,    0/0:3038:2991,0,47,0    ./.:0:0,0,0,0   ./.:0:0,0,0,0    0/0:3442:3321,6,115,    0/0:3596:3415,10,171    0/0:2965:2815,0,150,    0/0:2808:2655,0,153,    0/0:176:176,0,0,0        0/0:6595:6477,0,118,    ./.:0:0,0,0,0   ./.:0:0,0,0,0   0/0:61:61,0,0,0 0/0:3283:3196,0,87,0    0/0:4428:4371,0,57,0     0/0:71:71,0,0,0 0/0:2024:1985,1,38,0    0/0:855:795,0,60,0      0/0:2954:2932,0,22,0    0/0:5425:5344,0,81,0     0/0:3022:2892,0,130,    0/0:1541:1504,0,37,0    0/0:2816:2761,0,54,1    0/0:9:9,0,0,0   0/0:4713:4633,0,76,4    0/0:123:123,0,0,0        0/0:6447:6318,0,129,    0/0:55:55,0,0,0 0/0:1038:1020,0,18,0    0/0:3200:3138,0,62,0    0/0:7374:7144,9,221,     0/0:4679:4660,0,19,0    0/0:3064:2917,0,147,    0/0:2352:2300,1,51,0    0/0:538:538,0,0,0       0/0:117:117,0,0,0

Several have only 3 values in the CATG field where there should be 4.

Isaac Overcast
@isaacovercast
Aug 07 2018 22:21 UTC

Call for participation in the 1st New York Area RADCamp workshop presented by the Eaton Lab at Columbia University.

RADCamp workshops are designed to introduce ipyrad, a unified and self-contained RAD-Seq assembly and analysis framework, which emphasizes simplicity, performance, and reproducibility. In these workshops we proceed through all the steps necessary to assemble a typical RAD-Seq dataset. Additionally, we introduce the ipyrad ‘analysis’ API which provides a powerful, simple, and reproducible interface to several widely used methods for inferring phylogenetic relationships, population structure, and admixture.

The workshop will be presented over three days between August 28-30th at Columbia University. There will be a mix of facilitated instruction and hands on group work on targeted projects using both simulated and empirical data. Workshop participants will gain hands on experience in RAD-Seq assembly, phylogenetic and population genetic methods, high performance computing, basic unix command line and python programming, and jupyter notebooks to promote reproducible science. The preliminary schedule and workshop materials are available on the RADCamp website: https://radcamp.github.io/NYC2018/.

Participation will be limited to 30 individuals. Registration for this edition of RADCamp is $15, which will cover coffee and light snacks for the 3 day workshop. No one will be turned away for lack of funding. If you want to request a fee waiver please contact the organizers.

Register now for RADCamp 2018 NYC! https://www.eventbrite.com/e/radcamp-2018-new-york-city-edition-tickets-48820396119

RADCamp NYC is being organized and instruction will be provided by Dr Deren Eaton (Columbia), Isaac Overcast (CUNY/City College), & Dr Sandra Hoffberg (Columbia).

Isaac Overcast
@isaacovercast
Aug 07 2018 22:31 UTC
@yihanwu What version of ipyrad are you running?
yihanwu
@yihanwu
Aug 07 2018 22:34 UTC
0.7.23
Isaac Overcast
@isaacovercast
Aug 07 2018 22:44 UTC
Hm. Well it looks like in all cases that I can see the missing value is 0 anyway. Did you find any cases where the missing value isn't zero?
That is weird though.
yihanwu
@yihanwu
Aug 07 2018 22:51 UTC
I think the third individual? 1887+9+211
should be 2108?
and this one 0/0:5331:4897,0,432,
missing 2
maybe one of the bases was an "N" rather than "CATG" and so ipyrad doesn't know how to report it?