Entering edit mode
3.7 years ago
evelyn
▴
230
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!