vcf file format
1
1
Entering edit mode
2.0 years ago

Hi all,

I have been trying to convert my bam file to vcf file by using freebayes

This is the command I am using

freebayes -f genome.fa SRR1158613_hisat2_sorted.bam >SRR1158613.vcf 

where genome is the reference genome used

This is the error message I'm getting

index file genome.fa.fai not found, generating... 

I'm not understanding the error if anybody could help me with this

Thanks

freebayes vcf • 906 views
ADD COMMENT
1
Entering edit mode

genome.fa should have been indexed with samtools faidx genome.fa. It seems that it is just a warning and freebayes is able to do this itself.

your title "vcf file format" is unrelated to your problem.

ADD REPLY
0
Entering edit mode

i m sorry for that will take care from next time

ADD REPLY
0
Entering edit mode

yeah this worked but i was getting one more error

samtools error while loading shared libraries libncurses.so.5

and i solve this by

sudo apt-get install libncurses5n -64 bits

sudo apt-get install lib32z1

i think its irrelevant to what i questioned but i thought of posting this so if anybody gets such error can solve it

ADD REPLY
2
Entering edit mode
2.0 years ago
GenoMax 142k

That is not an error but a warning message. An index file for the genome is needed (created using samtools faidx genome.fa). If freebayes is unable to create it i.e. the process stalls then you can pre-create that in the directory where you genome is located by using samtools command above.

ADD COMMENT
0
Entering edit mode

I know you know , samtools index is for bam files :-)

ADD REPLY
0
Entering edit mode

Corrected :-)

ADD REPLY

Login before adding your answer.

Traffic: 1446 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6