apraga/org - Change 7IJA4MHKEW7A435DX4QEL7SL67TE5MYARTSIJVAY2ZD3QSCRILZQC

Bisonex update

Created by Alexis Praga on January 30, 2023

7IJA4MHKEW7A435DX4QEL7SL67TE5MYARTSIJVAY2ZD3QSCRILZQC

Dependencies

In channels

main

Change contents

Replacement in projects/bisonex.org at line 1327 [5.35]

B:BD[3.2931] → [4.14:1548]

|                     |       prod | prod Helios | prod Helios | prod Helios |       test |       test |       test |
|---------------------+------------+-------------+-------------+-------------+------------+------------+------------|
| cores               |          4 |           4 |          24 |           1 |         24 |         24 |          1 |
| gatk                |            |     4.2.4.1 |     4.2.4.1 |     4.2.4.1 |    4.2.4.1 |      4.3.0 |    4.2.3.1 |
| clinvar             | 2022-09-03 |  2022-09-03 |  2022-09-03 |  2022-09-03 | 2022-12-03 | 2022-12-03 | 2022-12-03 |
|---------------------+------------+-------------+-------------+-------------+------------+------------+------------|
| bwa mem             |  128077207 |   128077207 |   128077211 |   128077210 |  128077211 |  128077211 |  128077210 |
| cleanSam            |  128077207 |             |             |   128077210 |  128077211 |  128077211 |  128077210 |
| applybqsr           |            |             |   128077211 |             |            |            |            |
| haplotypecaller     |    1528059 |     1528066 |     1528093 |     1528089 |    1528093 |    1528093 |    1528093 |
| DP_over_30          |      84708 |             |       84724 |       84725 |      84724 |      84724 |      84725 |
| not_SNP             |      11362 |             |       11377 |       11384 |         NA |         NA |         NA |
| consensual_sequence |       8864 |             |        8884 |        8886 |       8898 |       8898 |       8900 |

[3.2931]

[3.4283]

|                     |       prod |      prod |       prod |       prod |       prod |       test |       test |       test |
|---------------------+------------+-----------+------------+------------+------------+------------+------------+------------|
| PC                  |     Karine |    helios |     helios |     helios |     Helios |     Helios |     Helios |     Helios |
| cores               |          4 |         4 |          4 |         24 |          1 |         24 |         24 |          1 |
| gatk                |    4.2.4.1 |   4.2.4.1 |    4.2.4.1 |    4.2.4.1 |    4.2.4.1 |    4.2.4.1 |      4.3.0 |    4.2.3.1 |
| samtools            |       1.10 |      1.10 |       1.13 |       1.13 |       1.13 |       1.13 |            |            |
| clinvar             | 2022-09-03 |           | 2022-09-03 | 2022-09-03 | 2022-09-03 | 2022-12-03 | 2022-12-03 | 2022-12-03 |
|---------------------+------------+-----------+------------+------------+------------+------------+------------+------------|
| bwa mem             |  128077207 | 128077207 |  128077207 |  128077211 |  128077210 |  128077211 |  128077211 |  128077210 |
| cleanSam            |  128077207 |           |            |            |  128077210 |  128077211 |  128077211 |  128077210 |
| applybqsr           |            |           |            |  128077211 |            |            |            |            |
| haplotypecaller     |    1528059 |   1528066 |    1528066 |    1528093 |    1528089 |    1528093 |    1528093 |    1528093 |
| DP_over_30          |      84708 |     84716 |      84716 |      84724 |      84725 |      84724 |      84724 |      84725 |
| not_SNP             |      11362 |     11366 |      11366 |      11377 |      11384 |         NA |         NA |         NA |
| consensual_sequence |       8864 |      8868 |       8868 |       8884 |       8886 |       8898 |       8898 |       8900 |

Replacement in projects/bisonex.org at line 2558 [5.35]

B:BD[2.16889] → [2.16889:16945]

***** TODO Relancer avec la même version de samtools ?

[2.16889]

[2.16945]


****** KILL Vérifier sha256sum
CLOSED: [2023-01-24 Tue 23:00]
alignment: différent
****** KILL Comparer bam
CLOSED: [2023-01-25 Wed 21:58]
/Work/Users/apraga/bisonex/script/files〉picard CompareSAMs LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_DUP=true tmp_63003856_S135/63003856_S135.bam /Work/Groups/bisonex/ref/tmp_63003856_S135/63003856_S135.bam O=compare-bam.tsv
picard CompareSAMs -LENIENT_LOW_MQ_ALIGNMENT true -LENIENT_DUP true tmp_63003856_S135/63003856_S135.bam /Work/Groups/bisonex/ref/tmp_63003856_S135/63003856_S135.bam -O compare-bam.tsv
VN Program Record attribute differs.
File 1: 1.13
File 2: 1.10
SAM files differ.
[Tue Jan 24 23:12:50 CET 2023] picard.sam.CompareSAMs done. Elapsed time: 7.32 minutes.
***** DONE Relancer avec la même version de samtools
CLOSED: [2023-01-25 Wed 21:58]
Pas d'impact
***** TODO Comparer tsv de sortie