About hg38 reference genome indexing

I tried to index reference genome fasta (hg38) that I downloaded UCSC version from below https://www.gungorbudak.com/blog/2018/05/16/how-to-download-hg38-grch38-fasta-human-reference-genome/

Used bwa, samtools(.fa.fai), picard(.dict)

Commands are

bwa index -a bwtsw hg38.fa

samtools faidx hg38.fa

java -Xmx2048m -jar path/to/picard.jar CreateSequenceDictionary -R hg38.fa -O hg38.dict

I found some weird chromosomes like these

@SQ SN:chr17_KI270729v1_random LN:280839
@SQ SN:chr1_KI270706v1_random LN:175055

Is this normal? or I did something wrong?

hg38 reference genome

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written 6.1 years ago by kwanghoon •

1 answer

See: A: Should I keep up with random contigs in human genome

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written 6.1 years ago by GenoMax

Thank you now I can understand..!

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written 6.1 years ago by kwanghoon •

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