-
```
What steps will reproduce the problem?
1. pysam-0.6
import pysam
import sys
# usage:
all_variants_vcf_fn = sys.argv[1]
vcf = pysam.VCF()
for ln in vcf.parse(open(all_variants_vcf_fn)):
…
-
CC @lbeltrame
Latest master.
Traceback:
```
[2015-05-07T13:50Z] uni17: Traceback (most recent call last):
[2015-05-07T13:50Z] uni17: File "/mnt/data/bcbio/anaconda/bin/gemini", line 6, in
[201…
-
Hi @ryan-williams @arahuja
```
please find the error when am trying to run the spark-submit.
```
16/05/02 14:59:37 INFO BlockManager: BlockManager stopped
16/05/02 14:59:37 IN…
-
```
What steps will reproduce the problem?
1. pysam-0.6
import pysam
import sys
# usage:
all_variants_vcf_fn = sys.argv[1]
vcf = pysam.VCF()
for ln in vcf.parse(open(all_variants_vcf_fn)):
…
-
We currently require that genotype likelihoods are _raw_ probabilities. However, many tools produce these likelihoods in other formats (e.g. as log-likelihoods). This feature will allow the specific…
rob-p updated
8 years ago
-
```
What steps will reproduce the problem?
1. pysam-0.6
import pysam
import sys
# usage:
all_variants_vcf_fn = sys.argv[1]
vcf = pysam.VCF()
for ln in vcf.parse(open(all_variants_vcf_fn)):
…
-
According to for format of GL(GL # Genotype log-likelihoods (natural log) for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites). How to get GL for multi-al…
-
## BUG
`make test` - CALL_Sample5.3_VCF_ALT fail under release mode but not debug mode
### How to reproduce it
Ran it twice, once in release, once in debug mode.
`cd build;`
**release mode**
`rm -r …
-
```
What steps will reproduce the problem?
1. pysam-0.6
import pysam
import sys
# usage:
all_variants_vcf_fn = sys.argv[1]
vcf = pysam.VCF()
for ln in vcf.parse(open(all_variants_vcf_fn)):
…
-
Hello,
I'm usign GPAT++ pFST function to get Fst Pvalues across populations.
I'have followed the instructions for installation and then used the program but an error ocurrs:
INFO: There are 11 indi…