Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • bcftools is printing <*> in the alt field

    Hello everybody.
    I am running bcftools on an mpileup file generated by samtools via the following command (I removed the paths and shortened the filenames for clarity):
    Code:
    samtools mpileup -E -uf hg19.fa accepted_hits.bam > accepted_hits.mpileup
    I then ran bcftools to identify the variation between the sample and the reference genome:
    Code:
    bcftools view -o file.vcf file.mpileup
    The resulting output file contains many lines with a <*> in the ALT column. Below is a small piece of the output file:

    Code:
    1	10497	.	C	<*>	0	.	DP=6;I16=4,2,0,0,237,9429,0,0,300,15000,0,0,136,3166,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,192
    1	10498	.	G	<*>	0	.	DP=6;I16=4,2,0,0,233,9117,0,0,300,15000,0,0,138,3240,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,190
    1	10499	.	G	<*>	0	.	DP=6;I16=4,2,0,0,237,9429,0,0,300,15000,0,0,140,3318,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,192
    1	10500	.	G	<*>	0	.	DP=6;I16=4,2,0,0,233,9117,0,0,300,15000,0,0,142,3400,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,190
    1	10501	.	T	<*>	0	.	DP=6;I16=4,2,0,0,218,8232,0,0,300,15000,0,0,144,3486,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,180
    1	10502	.	C	<*>	0	.	DP=6;I16=4,2,0,0,242,9774,0,0,300,15000,0,0,145,3525,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,197
    1	10503	.	T	<*>	0	.	DP=6;I16=4,2,0,0,238,9462,0,0,300,15000,0,0,146,3566,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,193
    1	10504	.	G	<*>	0	.	DP=6;I16=4,2,0,0,238,9462,0,0,300,15000,0,0,147,3609,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,193
    1	10505	.	A	<*>	0	.	DP=6;I16=4,2,0,0,246,10086,0,0,300,15000,0,0,148,3654,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,199
    1	10506	.	C	<*>	0	.	DP=6;I16=4,2,0,0,242,9774,0,0,300,15000,0,0,149,3701,0,0;QS=1,0;MQSB=1;MQ0F=0	PL	0,18,197
    I assume the <*> means there were no reads aligning to these positions of the genome.

    I tried various options such as "-U", "-m 2", "-c 1", but they either generated no output or did not do anything.

    What option do I use to prevent bcftools from printing the lines containing <*>?

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X