Comments (3)
Not entirely sure what is going on here. What version of Python are you using? If you are using 3.x can you try with 2.x?
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I tried Py27 and it worked. Thanks!. I do have another question where can I extract the information of which alleles have been phased? I want to see what percent of variants at a particular read depth are phased?
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Glad to hear that worked for you. As for your followup question, you can look in the outputted VCF or the haplotypes.txt file to determine which variants were phased. You'll need to do your own processing of those outputs to get the answer.
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Related Issues (20)
- How to use phaser without vcf file
- TypeError: a bytes-like object is required, not 'str HOT 3
- FATAL ERROR: No heterozygous sites that passed all filters were included in the analysis HOT 19
- phaser_gene_ae output with 0 Count? HOT 1
- Retrieve parent of origin for haplotypes HOT 1
- Advice on how to run phASER with RNA-seq data only and posed genotypes of parents HOT 1
- what kind of vcf file i can use?
- phASER error
- question regarding input vcf HOT 4
- version of phaser on github
- software is suitable for ChIP-seq data HOT 4
- Issues with phaser-pop HOT 2
- Container HOT 3
- phaser.py requires pysam HOT 1
- trying to locate phASER_GTEx_v8_merged.vcf.gz for phaser_cis_var.py (phaser-pop)
- Error in using phaser_gene_ae.py HOT 6
- parameter '--no_gw_phase 0' HOT 2
- phaser annotate module is still py2.7? HOT 3
- Recommendations for running phaser with just the rnaseq data HOT 3
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