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Unable to infer the A and B alleles while parsing the site...

11

I have a batch of VCF files from an array that I am trying to add ALLELE_A and ALLELE_B into to be able to run them through MoChA. I used...

AkshajD

Error [E::bgzf_read_block] Invalid BGZF header at offset 85619

1

Dear Giulio, When I run this command from the Mocha page on my data: ``` bcftools isec --no-version -Ou --complement --exclude "N_ALT>1" --write 1 $dir/$pfx.unphased.bcf $dir/$pfx.xcl.bcf | \ bcftools annotate...

IPriscilla

Use combined 1kG and HRC as reference panel for imputation

1

Hi! Is it possible to use HRC reference panel for imputation? Would it be possible for imputation to create reference panel that includes not only 1kG data but also Haplotype...

iranmdl

question regarding input.vcf

1

Hi, I need some help. Can I use bcftools mpileup for creating vcf file from bam files ? Or do I need to run germline caller like GATK or GATK...

beetlejuice007

trouble while installing MoCha

2

Hello, I'm getting trouble while installing MoCha with this command line. " cd bcftools-1.20/ /bin/rm -f plugins/{{mocha,beta_binom,genome_rules}.h,{mocha,mochatools,extendFMT}.c} wget -P plugins https://raw.githubusercontent.com/freeseek/mocha/master/{{mocha,beta_binom,genome_rules}.h,{mocha,mochatools,extendFMT}.c} make /bin/cp bcftools plugins/{fill-tags,fixploidy,mocha,trio-phase,mochatools,extendFMT}.so $HOME/bin/ " The error is...

zedicush