Off topic:freebayes problem in sample name in vcf
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7 months ago
evelyn ▴ 140

Hello,

I am using following command to create a vcf file with freebayes:

freebayes  -f  transcripts.fasta duplicates.bam --max-complex-gap         1 \
          --theta                   0.01 \
          --ploidy                  2 \
          --min-alternate-fraction  0.2 \
          --min-alternate-count     2 \
          --min-coverage            3 \
          --min-mapping-quality     1 \
          --min-base-quality        20 \
          --report-genotype-likelihood-max \
          --throw-away-complex-obs \
          --throw-away-mnps-obs \
          --throw-away-indel-obs > SNPs.vcf

I created the bam file using:

bwa mem transcripts.fastaR1_paired.fastq.gz R2_paired.fastq.gz > paired_bwa.sam
samtools view -S -b paired_bwa.sam > paired_bwa.bam
samtools sort -o paired_bwa.bam -O bam paired_bwa.sorted.bam
samtools index paired_bwa.sorted.bam

but the vcf file does not show sample name in the header, it shows unknown:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  unknown

I want the sample name to show instead of unknown. Thank you!

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